debian/0000755000000000000000000000000012214054517007167 5ustar debian/emboss-doc.doc-base.emboss-apps0000644000000000000000000000050112214054043015037 0ustar Document: emboss-apps Title: EMBOSS Applications Author: The EMBOSS Developpers Section: Science/Biology Abstract: Documentation of the EMBOSS applications sorted in alphabetical order. Format: HTML Index: /usr/share/doc/emboss-doc/doc/programs/html/index.html Files: /usr/share/doc/emboss-doc/doc/programs/html/*.html debian/gbp.conf0000644000000000000000000000033212214054043010576 0ustar # The source package of emboss is managed with git-buildpackage and pristine-tar. [DEFAULT] # use pristine-tar: pristine-tar = True [git-dch] # include 7 digits of the commit ID in the changelog entry: id-length = 7 debian/control0000644000000000000000000001106312214054043010565 0ustar Source: emboss Maintainer: Debian Med Packaging Team Uploaders: Charles Plessy , Nelson A. de Oliveira , Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9), quilt, libx11-dev, x11proto-core-dev, libgdchart-gd2-xpm-dev, zlib1g-dev, libpng-dev, libexpat1-dev, libhpdf-dev, libmysqlclient-dev, libpq-dev, antiword, sharutils, autotools-dev, tcsh | csh | c-shell, dh-autoreconf, # Needed until the following is solved: https://sourceforge.net/tracker/?func=detail&aid=3033326&group_id=93650&atid=605031 default-jdk #Build-Depends-Indep: default-jdk Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debian-med/emboss.git Vcs-Git: git://anonscm.debian.org/debian-med/emboss.git Homepage: http://emboss.sourceforge.net Package: emboss Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, emboss-lib (= ${binary:Version}), emboss-data (= ${source:Version}) Recommends: primer3, dialign Suggests: emboss-doc, emboss-test, embassy, clustalw Description: european molecular biology open software suite EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages. Package: emboss-data Architecture: all Depends: ${misc:Depends} Description: data files for the EMBOSS package This package includes data files needed by EMBOSS, the European Molecular Biology Open Software Suite. Package: emboss-doc Architecture: all Section: doc Depends: ${misc:Depends} Suggests: evince | pdf-viewer | postscript-viewer Description: documentation for EMBOSS This package includes non-essential user documentation for EMBOSS, the European Molecular Biology Open Software Suite. Package: emboss-test Architecture: all Section: misc Depends: ${misc:Depends} Recommends: tcsh | csh | c-shell Suggests: valgrind Description: test files for the EMBOSS package This package includes test files for EMBOSS, the European Molecular Biology Open Software Suite. . It is a good idea to use the data from this package for your bug reports when possible. Package: emboss-lib Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Conflicts: libajax5, libajax6, libajax5-dev, libajax6-dev, libnucleus5, libnucleus6, libnucleus5-dev, libnucleus6-dev Replaces: libajax5, libajax6, libajax5-dev, libajax6-dev, libnucleus5, libnucleus6, libnucleus5-dev, libnucleus6-dev Description: EMBOSS Libraries This package contains the core libraries of the European Molecular Biology Open Software Suite, EMBOSS. . AJAX covers standard data structures, including strings, sequences, file handles, queues, hashes, heaps, lists, dictionaries, trees and dynamic arrays. It also covers standard algorithms including comparisons, pattern matching, sorting, and iterators. AJAX will also provide a set of high level graphics functions suited to the needs of sequence analysis applications. . The NUCLEUS library provides higher-level functions specific to molecular sequence analysis, including sequence comparisons, translation, codon usage and annotation. . It also contains a eplplot, an EMBOSS, a fork of the plplot library. . In Debian, these libraries are to be considered private. Package: jemboss Architecture: all Depends: ${shlibs:Depends}, ${misc:Depends}, emboss, default-jre, tcsh | csh | c-shell Description: graphical user interface to EMBOSS Jemboss is a Graphical User Interface (GUI) to EMBOSS, the European Molecular Biology Open Software Suite. It is part of the EMBOSS distribution. debian/emboss-doc.links0000644000000000000000000000006212214054043012254 0ustar usr/share/EMBOSS/doc usr/share/doc/emboss-doc/doc debian/emboss.sharedmimeinfo0000644000000000000000000000203512214054043013365 0ustar ABIF chromatogram ABIF Applied Biosystems, Inc. Format debian/jemboss.dirs0000644000000000000000000000001112214054043011476 0ustar /usr/bin debian/EMBOSS_qg.doc.uu0000644000000000000000000026033012214054043011763 0ustar begin 644 EMBOSS_qg.doc MT,\1X*&Q&N$`````````````````````/@`#`/[_"0`&```````````````! M````>P``````````$```?0````$```#^____`````'H```#_____________ M____________________________________________________________ M____________________________________________________________ M____________________________________________________________ M____________________________________________________________ M____________________________________________________________ M____________________________________________________________ M____________________________________________________________ M____________________________________________________________ M____________________________________________________________ M_______________________LI<$`!V$)!```\!*_```````!$0`!``$`!@`` M3B\```X`:F)J8H0LA"P````````````````````````)!!8`DG4``.Y.``#N M3@``3BD```````````````````````````````````````#__P\````````` M``#__P\```````````#__P\``````````````````````(@``````#8#```` M````-@,``#8#````````-@,````````V`P```````#8#````````-@,``!0` M`````````````*X#````````UC4```````#6-0```````-8U````````UC4` M`"P````"-@``3````*X#````````OT<``'@!``!:-@```````%HV```````` M6C8```````!:-@```````%HV````````6C8```````!:-@```````%HV```` M````-D<```(````X1P```````#A'````````.$<````````X1P```````#A' M````````.$<``"P````W20``4@(``(E+``!.````9$<``!4````````````` M````````````-@,```````!:-@````````````````````````````!:-@`` M`````%HV````````6C8```````!:-@```````&1'````````-D<````````V M`P```````#8#````````6C8``````````````````%HV````````>4<``!8` M```V1P```````#9'````````-D<```````!:-@``)@@``#8#````````6C8` M```````V`P```````%HV````````-D<``````````````````#9'```````` M2@,``"0```!N`P``0````#8#````````-@,````````V`P```````#8#```` M````6C8````````V1P``````````````````-D<``````````````````#9' M````````-@,````````V`P`````````````````````````````````````` M````````````````````````````````````````````-D<````````````` M`````$XV```,````-D0QPP```````````````-8U````````@#X``+8(```V M1P``````````````````-D<```````"/1P``,````+]'````````-D<````` M``#72P```````#9'````````UTL````````V1P```````#9'```````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````V`P`````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M`````````````````````````````````*X#````````K@,``,0>``!R(@`` M9!,```````````````````````"N`P```````*X#````````2!/<&5N(%-O9G1W87)E(%-U:71E M#0U(:7-T;W)Y#5-I;F-E(#$Y.#@L('1H92!S97%U96YC92!A;F%L>7-I2!N M97<@9V5N97)A=&EO;B!O9B!A8V%D96UI8R!S97%U96YC92!A;F%L>7-I6EN9RP-;6]D:69I8V%T:6]N(&%N M9"!D:7-T7-T96T-861M:6YI6]U2!T>7!E6]U#7=I;&P@8F4@<')O;7!T960@:68@>6]U('5S92!T:&4@EF]P=&EO;B!Q M=6%L:69I97(N($%L;"!T:&5S90UQ=6%L:69I97)S(&AA=F4@9&5F875L="!V M86QU97,N#4%D=F%N8V5D(%%U86QI9FEE7!E7!E($%L;&]W960@=F%L=65S#6)O;VP@ M>65S.B`M<&%R86T@;F\Z("UN;W!A"!F;W(@ M86QI9VYM96YT6=R87!H(&]U='!U M="!D979I8V4@9F]R(%A9(&=R87!H2!O9B!T:&5S92X-#D%S'1E;G-I;VX@6=R87!H#2UG<')O;7!T(&)O;VP@9W)A<&@@<')O;7!T:6YG M#2UG=&ET;&4@'1I=&QE('-T3(I('1I=&QE#2UG<&%G97,@:6YT96=E2!I;F9O61O="!S=7!E2!O9B!P;W1E;G1I86P@3U)&"!A;F0@2VT@8V%L8W5L871I;VYS#69U>GIP2!%34)/4U,-#4EN=&5L;&E'96YE=&EC2!A;F0@:7,@8V]P>7)I9VAT($1R($1A M=FED#4UA2!B92!C;W!I960@86YD M(&1I#0``0`X``%X.``!B#@``<0X``*8.``"N M#@``VPX``.0.```L#P``,P\``&4/``!R#P``XP\``.H/``!W$```FQ```-40 M``#=$```]1```/X0```$$0``#A$``#81```\$0``;A$``(<1``"*$@``GQ(` M`!\3``#GSK6>M9ZUGH>UA[6>M9YNGK6>;IYNGK6>;IZUGK6>M9ZUGK6>M9ZU MGK6>`#`5:($3;``6:)(XX@`V"(%"*@%#2A(`3TH#`%%*`P!A2A(`;4@)!'!H M`````'-("00`+15H@1-L`!9HDCCB`$(J`D-*$@!/2@,`44H#`&%*$@!M2`D$ M<&@``/\`"P``;PL``*H+``#D M"P``"PP``/0```````````````#T````````````````]``````````````` M`/0```````````````#T````````````````]````````````````/0````` M``````````#T````````````````]````````````````/0````````````` M``#T````````````````]````````````````/0```````````````#T```` M````````````]````````````````/0```````````````#T```````````` M````]````````````````/0```````````````#T````````````````]``` M`````````````/0```````````````#T````````````````]``````````` M`````/0```````````````#T````````````````]````````````````/0` M```````````````````````````*```Q)``W)``X)`!()`!G9)(XX@``'``& M``!.+P``_@`````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````"`0$!"PP``!H,``!.#```B0P``,@,```�``-0T``&\- M``"N#0``N@T``-X-```;#@``0`X``%X.``!Q#@``*@\``#,/``!A#P``G`\` M`-D/```5$```3A```'<0``"+$```FQ```-40```$$0``(Q$``#81``#T```` M````````````]````````````````/0```````````````#T```````````` M````]````````````````/0```````````````#T````````````````]``` M`````````````/0```````````````#T````````````````]``````````` M`````/0```````````````#T````````````````]````````````````/0` M``````````````#T````````````````]````````````````/0````````` M``````#T````````````````]````````````````/0```````````````#T M````````````````]````````````````/0```````````````#T```````` M````````]````````````````/0```````````````#T```````````````` M````````````"@``,20`-R0`."0`2"0`9V22..(``!PV$0``5A$``&P1``"' M$0``P!$``.P1```I$@``8Q(``(H2``"?$@``V1(``!D3```?$P``21,``'03 M``"($P``O1,``.L3```'%```-Q0``$84``!Z%```B!0``+44``#&%```W!0` M``86```;%@``EA8``/0```````````````#T````````````````]``````` M`````````/0```````````````#T````````````````]``````````````` M`/0```````````````#T````````````````]````````````````/0````` M``````````#T````````````````]````````````````/0````````````` M``#T````````````````]````````````````/0```````````````#T```` M````````````]````````````````/0```````````````#T```````````` M````]````````````````/0```````````````#T````````````````]``` M`````````````/0```````````````#T````````````````]``````````` M`````/0````````````````````````````*```Q)``W)``X)`!()`!G9)(X MX@``'!\3```E$P``8!,``&D3``"($P``D1,``+T3``##$P``!Q0```T4``!& M%```3A0``(@4``"0%```QA0``-P4``#@%```YA0``'P5``"%%0``!A8``!L6 M``"0%@``JA8``.T6``#U%@``*A<``#X7``"G%P``OA<``-(7``#7%P``W!<` M`.,7``#G%P``^!<```88```5&```)1@``#<8``!,&```91@``((8``")&``` MF!@``+08``##&```RA@``/`8``#X&```%AD``!P9```N&0``11D``(H9``"3 M&0``H1D``*89``"V&0``P!D``-H9``#B&0``"!H```\:```C&@``+1H``$\: M``!9&@``@AH``(H:``"?&@``I1H``,<:``#/&@``&!L``.?0Y]#GT.?0Y]#G MT.?0Y]#GT.?0Y]#GT.?0Y]#GT.?0Y]#GT.?0Y]#GT.?0Y]#GT.?0Y]#GT.?0 MY]#GT.?0Y]#GT.?0Y]#GT.?0```````````````````````````````````` M````````````````````+15H@1-L`!9HDCCB`$(J`4-*$@!/2@,`44H#`&%* M$@!M2`D$<&@```````!H M'@``B1X``*H>``#*'@``]````````````````/0```````````````#L```` M````````````]````````````````/0```````````````#T```````````` M````]````````````````/0```````````````#T````````````````]``` M`````````````/0```````````````#T````````````````]``````````` M`````/0```````````````#T````````````````]````````````````/0` M``````````````#T````````````````]````````````````/0````````` M``````#T````````````````]````````````````/0```````````````#T M````````````````]````````````````/0```````````````#T```````` M``````````````````````<``#$D`#!L``)4;``"?&P``N1L` M`+\;``#E&P``\AL``!(<```<'```.1P``$$<``!A'```:1P``(D<``"2'``` MKQP``+H<``#0'```V1P``.X<``#V'```&1T``!X=```Y'0``0AT``%D=``!R M'0``C1T``)<=``"U'0``PAT``-P=``#D'0``^1T```,>```?'@``*1X``$X> M``!4'@``:!X``'(>``")'@``D1X``*H>``#3'@``ZAX``/4>```.'P``%!\` M`"0?```R'P``-A\``$```.'P``/Q\``&H? M``".'P``P!\``-\?``#_'P``(B```$D@``!A(```BR```+$@``#/(```ZB`` M``LA```H(0``12$``&LA``"+(0``K"$``,$A``#Z(0``6B(``'$B``#=(@`` M_"(``!HC``#T````````````````]````````````````/0````````````` M``#T````````````````]````````````````/0```````````````#T```` M````````````]````````````````/0```````````````#T```````````` M````]````````````````/0```````````````#T````````````````]``` M`````````````/0```````````````#T````````````````]``````````` M`````/0```````````````#T````````````````]````````````````/0` M``````````````#T````````````````]````````````````/0````````` M``````#T````````````````]````````````````/0```````````````#T M````````````````````````````"@``,20`-R0`."0`2"0`9V22..(``!QK M(```BR```+H@``#/(```UR```.H@``#U(```"R$``!0A```H(0``,2$``$4A M``!.(0``:R$``',A``"+(0``E2$``*PA``#!(0``6B(``'$B``#\(@``!",` M`!HC```E(P``:",``&PC``"/(P``E",``*HC``"O(P``_2,```4D```U)``` M/20``%LD``!E)```RB0``,XD``#/)```UB0``-HD```+)0``)24``"PE``!* M)0``9"4``)(E``"F)0``YB4``.XE```2)@``'B8``$(F``!-)@``;28``'0F M``"4)@``G28``,8F``#.)@``\R8``/PF```D)P``/R<``&(G``!H)P``BB<` M`)0G``"V)P``OB<``-\G``#Q)P``Z,_HS^C/Z,_HS^C/Z,_HS^C/Z,_HS^C/ MZ,_HS^C/Z,_HS^C/Z+;HMNC/Z,_HS^C/Z,_HS^C/Z,_HS^C/Z,_HS^C/Z,_H MS^C/,!5H@1-L`!9HDCCB`#8(@4(J`4-*$@!/2@,`44H#`&%*$@!M2`D$<&@` M````*``` MXB@```DI```1*0``+2D``$DI``!I*0``?"D``)$I``"D*0``QBD``,XI``#C M*0``ZRD```PJ```4*@``)RH``"XJ``!2*@``<"H``(XJ``"8*@``N"H``+\J M``#5*@``W"H``/4J``#]*@``%"L``!PK```\*P``2RL``&TK``"`*P``G"L` M`+(K``#=*P``Y2L```(L```4+```*"P``#$L``!5+```Y2P``,PM``#G+0`` MU2X``$PO``!-+P``3B\``.C/Z,_HS^C/Z,_HS^C/Z,_HS^C/Z,_HS^C/Z,_H MS^C/Z,_HS^C/Z,_HS^C/Z,_HS^C/Z,_HN.BXZ+0````````````````````` M```````````````````````````````````````````````````````````` M```````&%FB2..(``"T5:($3;``6:)(XX@!"*@)#2A(`3TH#`%%*`P!A2A(` M;4@)!'!H``#_`'-("00P%6B!$VP`%FB2..(`-0B!0BH!0TH2`$]*`P!12@,` M84H2`&U("01P:`````!S2`D$`"T5:($3;``6:)(XX@!"*@%#2A(`3TH#`%%* M`P!A2A(`;4@)!'!H`````'-("00`.FTK``"<*P``I2L``-TK```"+```*"P` M`%4L``!6+```=RP``'@L``"O+```Y2P``.8L```@+0``?"T``+@M``#G+0`` MB"X``,4N``#K+@``["X``$PO``!-+P``3B\``/0```````````````#T```` M````````````]````````````````/0```````````````#T```````````` M````]````````````````/0```````````````#T````````````````]``` M`````````````/0```````````````#T````````````````]``````````` M`````/0```````````````#T````````````````]````````````````/0` M``````````````#T````````````````]````````````````/0````````` M``````#T````````````````]````````````````/(```````````````#R M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M`````````````````0````H``#$D`#P```8 ML```"U`"`%@C``P``P```2P!+``````)3`U/_\__S0E^#8$#905[`^```@`` M`$@`2``````"V`(H``$```!D`````0`#`P,````!?_\``0`!```````````` M````:`@`&0&0```````@```````````````````````````````````\/WAM M;"!V97)S:6]N/2(Q+C`B(&5N8V]D:6YG/2)55$8M."(_/@H\(41/0U194$4@ M<&QI3YC;VTN87!P;&4N<')I;G0N4&%G949O3YC;VTN87!P;&4N<')I;G0N=&EC:V5T M+F-R96%T;W(\+VME>3X*"0D\3X*"0D)"3QS=')I;F<^;&%S97)?-34P,%]O;E]H<#4U,#`N8V]M<&)I M;RYD=6YD964N86,N=6L\+W-T3X*"0D)"3QD871E/C(P,#3YC;VTN87!P;&4N<')I;G0N M=&EC:V5T+G-T871E1FQA9SPO:V5Y/@H)"0D)/&EN=&5G97(^,#PO:6YT96=E M3YC;VTN87!P;&4N<')I;G0N=&EC:V5T+F-R96%T;W(\ M+VME>3X*"0D\F]N=&%L4F5S/"]K97D^"@D)"0D\ M3YC;VTN87!P;&4N<')I M;G0N4&%G949O3YC;VTN87!P;&4N<')I;G0N=&EC:V5T+F-L:65N M=#PO:V5Y/@H)"0D)/'-T3X*"3PO9&EC=#X*"3QK97D^8V]M+F%P<&QE+G!R:6YT+E!A9V5& M;W)M870N4$U38V%L:6YG/"]K97D^"@D\9&EC=#X*"0D\:V5Y/F-O;2YA<'!L M92YP3YC;VTN87!P;&4N<')I;G0N4&%G949O3YC;VTN87!P;&4N M<')I;G0N4&%G949O3YC;VTN87!P;&4N<')I;G0N=&EC:V5T+F-R96%T;W(\+VME M>3X*"0D\3X*"0D)"3QR M96%L/C$\+W)E86P^"@D)"0D\:V5Y/F-O;2YA<'!L92YP3YC;VTN87!P;&4N<')I;G0N M3YC;VTN87!P;&4N<')I;G0N M=&EC:V5T+FET96U!3PO:V5Y/@H)"0D\87)R87D^"@D)"0D\9&EC=#X* M"0D)"0D\:V5Y/F-O;2YA<'!L92YP3X*"0D)"0D)/')E86P^,"XP M/"]R96%L/@H)"0D)"0D\3YC;VTN M87!P;&4N<')I;G0N=&EC:V5T+F-L:65N=#PO:V5Y/@H)"0D)"3QS=')I;F<^ M8V]M+F%P<&QE+G!R:6YT:6YG;6%N86=E3YC;VTN M87!P;&4N<')I;G0N=&EC:V5T+G-T871E1FQA9SPO:V5Y/@H)"0D)"3QI;G1E M9V5R/C`\+VEN=&5G97(^"@D)"0D\+V1I8W0^"@D)"3PO87)R87D^"@D)/"]D M:6-T/@H)"3QK97D^8V]M+F%P<&QE+G!R:6YT+E!A9V5&;W)M870N4$U!9&IU M3YC;VTN87!P M;&4N<')I;G0N=&EC:V5T+FET96U!3PO:V5Y/@H)"0D\87)R87D^"@D) M"0D\9&EC=#X*"0D)"0D\:V5Y/F-O;2YA<'!L92YP3X*"0D)"0D\87)R87D^"@D)"0D) M"3QR96%L/BTT.2XV-C8U.34T-3@Y.#0S-S4\+W)E86P^"@D)"0D)"3QR96%L M/BTU,2XS,S,S-C,X-3`Y,3$T-C$\+W)E86P^"@D)"0D)"3QR96%L/C(T,CDN M-3`P,#3YC;VTN87!P M;&4N<')I;G0N=&EC:V5T+F-L:65N=#PO:V5Y/@H)"0D)"3QS=')I;F<^8V]M M+F%P<&QE+G!R:6YT:6YG;6%N86=E3YC;VTN87!P M;&4N<')I;G0N=&EC:V5T+G-T871E1FQA9SPO:V5Y/@H)"0D)"3QI;G1E9V5R M/C`\+VEN=&5G97(^"@D)"0D\+V1I8W0^"@D)"3PO87)R87D^"@D)/"]D:6-T M/@H)"3QK97D^8V]M+F%P<&QE+G!R:6YT+E!A<&5R26YF;RY034-U3X*"0D)"3QD:6-T/@H) M"0D)"3QK97D^8V]M+F%P<&QE+G!R:6YT+E!A<&5R26YF;RY034-U3YC;VTN87!P M;&4N<')I;G0N=&EC:V5T+FUO9$1A=&4\+VME>3X*"0D)"0D\9&%T93XR,#`W M+3$P+3`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`N,#PO3X*"0D)"3QD:6-T/@H)"0D)"3QK97D^8V]M+F%P<&QE+G!R:6YT M+E!A<&5R26YF;RY0355N861J=7-T961087!E3X*"0D)"0D\ M87)R87D^"@D)"0D)"3QR96%L/BTQ,BXS,C`P,#3X*"0D)"3QD:6-T/@H)"0D)"3QK97D^8V]M+F%P<&QE M+G!R:6YT+E!A<&5R26YF;RYP<&0N4$U087!E3X*"0D)"0D\ M3YC;VTN87!P;&4N<')I;G0N M=&EC:V5T+G-T871E1FQA9SPO:V5Y/@H)"0D)"3QI;G1E9V5R/C$\+VEN=&5G M97(^"@D)"0D\+V1I8W0^"@D)"3PO87)R87D^"@D)/"]D:6-T/@H)"3QK97D^ M8V]M+F%P<&QE+G!R:6YT+G1I8VME="Y!4$E697)S:6]N/"]K97D^"@D)/'-T M3YC;VTN M87!P;&4N<')I;G0N=&EC:V5T+G1Y<&4\+VME>3X*"0D\ M!P``&P@``$`(``!>"```<0@``"H)```S"0``80D``)P)``#9"0``%0H``$X* M``!W"@``BPH``)L*``#5"@``!`L``",+```V"P``5@L``&P+``"'"P``P`L` M`.P+```I#```8PP``(H,``"?#```V0P``!D-```?#0``20T``'0-``"(#0`` MO0T``.L-```'#@``-PX``$8.``!Z#@``B`X``+4.``#&#@``W`X```80```; M$```EA```,T0```*$0``*A$``%T1``"9$0``IQ$``+X1``#2$0``\!$```\2 M```Q$@``7A(``((2``"M$@``PQ(``/`2```6$P``+A,``(H3``"A$P``MA,` M`-H3```(%```(Q0``$\4``""%```GQ0``,<4``#K%```&14``$H5``!R%0`` ME14``+D5``#E%0``$A8``#D6``!A%@``B18``*\6``#0%@``[A8``!D7```Y M%P``61<``(T7``"U%P``W!<``/D7```?&```3A@``&@8``")&```JA@``,H8 M``#J&```#AD``#\9``!J&0``CAD``,`9``#?&0``_QD``"(:``!)&@``81H` M`(L:``"Q&@``SQH``.H:```+&P``*!L``$4;``!K&P``BQL``*P;``#!&P`` M^AL``%H<``!Q'```W1P``/P<```:'0``2QT``&@=``"/'0``JAT``/T=```U M'@``6QX``'\>``"R'@``Y1X``/H>```"'P``)1\``$H?``!='P``DA\``-$? M``#F'P``$B```$(@``!M(```E"```,8@``#S(```)"$``#@A``!B(0``BB$` M`+8A``#?(0``YB$``/$A```7(@``12(``(4B``":(@``O2(``-XB```)(P`` M+2,``$,C``!I(P``D2,``,8C``#C(P``#"0``" M@`"8`````#``````````@````(````"0````RH``F``````P`````````(`` M``"`````D````,J``)@`````,`````````"`````@````)````#*@`"8```` M`#``````````@````(````"0````RH``F``````P`````````(````"````` MD````,J``)@`````,`````````"`````@````)````#*@`"8`````#`````` M````@````(````"0````RH``F``````P`````````(````"`````D````,J` M`)@`````,`````````"`````@````)````#*@`"8`````#``````````@``` M`(````"0````RH``F``````P`````````(````"`````D````,J``)@````` M,`````````"`````@````)````#*@`"8`````#``````````@````(````"0 M````RH``F``````P`````````(````"`````D````,J``)@`````,``````` M``"`````@````)````#*@`"8`````#``````````@````(````"0````RH`` MF``````P`````````(````"`````D````,J``)@`````,`````````"````` M@````)````#*@`"8`````#``````````@````(````"0````RH``F``````P M`````````(````"`````D````,J``)@`````,`````````"`````@````)`` M``#*@`"8`````#``````````@````(````"0````RH``F``````P```````` M`(````"`````D````,J``)@`````,`````````"`````@````)````#*@`"8 M`````#``````````@````(````"0````RH``F``````P`````````(````"` M````D````,J``)@`````,`````````"`````@````)````#*@`"8`````#`` M````````@````(````"0````RH``F``````P`````````(````"`````D``` M`,J``)@`````,`````````"`````@````)````#*@`"8`````#`````````` M@````(````"0````RH``F``````P`````````(````"`````D````,J``)@` M````,`````````"`````@````)````#*@`"8`````#``````````@````(`` M``"0````RH``F``````P`````````(````"`````D````,J``)@`````,``` M``````"`````@````)````#*@`"8`````#``````````@````(````"0```` MRH``F``````P`````````(````"`````D````,J``)@`````,`````````"` M````@````)````#*@`"8`````#``````````@````(````"0````RH``F``` M```P`````````(````"`````D````,J``)@`````,`````````"`````@``` M`)````#*@`"8`````#``````````@````(````"0````RH``F``````P```` M`````(````"`````D````,J``)@`````,`````````"`````@````)````#* M@`"8`````#``````````@````(````"0````RH``F``````P`````````(`` M``"`````D````,J``)@`````,`````````"`````@````)````#*@`"8```` M`#``````````@````(````"0````RH``F``````P`````````(````"````` MD````,J``)@`````,`````````"`````@````)````#*@`"8`````#`````` M````@````(````"0````RH``F``````P`````````(````"`````D````,J` M`)@`````,`````````"`````@````)````#*@`"8`````#``````````@``` M`(````"0````RH``F``````P`````````(````"`````D````,J``)@````` M,`````````"`````@````)````#*@`"8`````#``````````@````(````"0 M````RH``F``````P`````````(````"`````D````,J``)@`````,``````` M``"`````@````)````#*@`"8`````#``````````@````(````"0````RH`` MF``````P`````````(````"`````D````,J``)@`````,`````````"````` M@````)````#*@`"8`````#``````````@````(````"0````RH``F``````P M`````````(````"`````D````,J``)@`````,`````````"`````@````)`` M``#*@`"8`````#``````````@````(````"0````RH``F``````P```````` M`(````"`````D````,J``)@`````,`````````"`````@````)````#*@`"8 M`````#``````````@````(````"0````RH``F``````P`````````(````"` M````D````,J``)@`````,`````````"`````@````)````#*@`"8`````#`` M````````@````(````"0````RH``F``````P`````````(````"`````D``` M`,J``)@`````,`````````"`````@````)````#*@`"8`````#`````````` M@````(````"0````RH``F``````P`````````(````"`````D````,J``)@` M````,`````````"`````@````)````#*@`"8`````#``````````@````(`` M``"0````RH``F``````P`````````(````"`````D````,J``)@`````,``` M``````"`````@````)````#*@`"8`````#``````````@````(````"0```` MRH``F``````P`````````(````"`````D````,J``)@`````,`````````"` M````@````)````#*@`"8`````#``````````@````(````"0````RH``F``` M```P`````````(````"`````D````,J``)@`````,`````````"`````@``` M`)````#*@`"8`````#``````````@````(````"0````RH``F``````P```` M`````(````"`````D````,J``)@`````,`````````"`````@````)````#* M@`"8`````#``````````@````(````"0````RH``F``````P`````````(`` M``"`````D````,J``)@`````,`````````"`````@````)````#*@`"8```` M`#``````````@````(````"0````RH``F``````P`````````(````"````` MD````,J``)@`````,`````````"`````@````)````#*@`"8`````#`````` M````@````(````"0````RH``F``````P`````````(````"`````D````,J` M`)@`````,`````````"`````@````)````#*@`"8`````#``````````@``` M`(````"0````RH``F``````P`````````(````"`````D````,J``)@````` M,`````````"`````@````)````#*@`"8`````#``````````@````(````"0 M````RH``F``````P`````````(````"`````D````,J``)@`````,``````` M``"`````@````)````#*@`"8`````#``````````@````(````"0````RH`` MF``````P`````````(````"`````D````,J``)@`````,`````````"````` M@````)````#*@`"8`````#``````````@````(````"0````RH``F``````P M`````````(````"`````D````,J``)@`````,`````````"`````@````)`` M``#*@`"8`````#``````````@````(````"0````RH``F``````P```````` M`(````"`````D````,J``)@`````,`````````"`````@````)````#*@`"8 M`````#``````````@````(````"0````RH``F``````P`````````(````"` M````D````,J``)@`````,`````````"`````@````)````#*@`"8`````#`` M````````@````(````"0````RH``F``````P`````````(````"`````D``` M`,J``)@`````,`````````"`````@````)````#*@`"8`````#`````````` M@````(````"0````RH``F``````P`````````(````"`````D````,J``)@` M````,`````````"`````@````)````#*@`"8`````#``````````@````(`` M``"0````RH``F``````P`````````(````"`````D````,J``)@`````,``` M``````"`````@````)````#*@`"8`````#``````````@````(````"0```` MRH``F``````P`````````(````"`````D````,J``)@`````,`````````"` M````@````)````#*@`"8`````#``````````@````(````"0````RH``F``` M```P`````````(````"`````D````,J``)@`````,`````````"`````@``` M`)````#*@`"8`````#``````````@````(````"0````RH``F``````P```` M`````(````"`````D````,J``)@`````,`````````"`````@````)````#* M@`"8`````#``````````@````(````"0````RH``F``````P`````````(`` M``"`````D````,J``)@`````,`````````"`````@````)````#*@`"8```` M`#``````````@````(````"0````RH``F``````P`````````(````"````` MD````,J``)@`````,`````````"`````@````)````#*@`"8`````#`````` M````@````(````"0````RH``F``````P`````````(````"`````D````,J` M`)@`````,`````````"`````@````)````#*@`"8`````#``````````@``` M`(````"0````RH``F``````P`````````(````"`````D````,J``)@````` M,`````````"`````@````)````#*@`"8`````#``````````@````(````"0 M````RH``F``````P`````````(````"`````D````,J``)@`````,``````` M``"`````@````)````#*@`"8`````#``````````@````(````"0````RH`` MF``````P`````````(````"`````D````,J``)@`````,`````````"````` M@````)````#*@`"8`````#``````````@````(````"0````RH``F``````P M`````````(````"`````D````,J``)@`````,`````````"`````@````)`` M``#*@`"8`````#``````````@````(````"0````RH``F``````P```````` M`(````"`````D````,J``)@`````,`````````"`````@````)````#*@`"8 M`````#``````````@````(````"0````RH``F``````P`````````(````"` M````D````,J``)@`````,`````````"`````@````)````#*@`"8`````#`` M````````@````(````"0````RH``F``````P`````````(````"`````D``` M`,J``)@`````,`````````"`````@````)````#*@`"8`````#`````````` M@````(````"0````RH``F``````P`````````(````"`````D````,J``)@` M````,`````````"`````@````)````#*@`"8`````#``````````@````(`` M``"0````RH``F``````P`````````(````"`````D````,J``)@`````,``` M``````"`````@````)````#*@`"8`````#``````````@````(````"0```` MRH``F``````P`````````(````"`````D````,J``)@`````,`````````"` M````@````)````#*@`"8`````#``````````@````(````"0````RH``F``` M```P`````````(````"`````D````,J``)@`````,`````````"`````@``` M`)````#*@`"8`````#``````````@````(````"0````RH``F``````P```` M`````(````"`````D````,J``)@`````,`````````"`````@````)````#* M@`"8`````#``````````@````(````"0````RH``F``````P`````````(`` M``"`````D````,J``)@`````,`````````"`````@````)````#*@`"8```` M`#``````````@````(````"0````RH``F``````P`````````(````"````` MD````,J``)@`````,`````````"`````@````)````#*@`"8`````#`````` M````@````(````"0````RH``F``````P`````````(````"`````D````,J` M`)@`````,`````````"`````@````)````#*@`"8`````#``````````@``` M`(````"0````RH``F``````P`````````(````"`````D````,J``)@````` M,`````````"`````@````)````#*@`"8`````#``````````@````(````"0 M````RH``F``````P`````````(````"`````D````,J``)@`````,``````` M``"`````@````)````#*@`"8`````#``````````@````(````"0````RH`` MF``````P`````````(````"`````D````,J``)@`````,`````````"````` M@````)````#*@`"8`````#``````````@````(````"0````RH``F``````P M`````````(````"`````D````,J``)@`````,`````````"`````@````)`` M``#*@`"8`````#``````````@````(````"0````RH``F``````P```````` M`(````"`````D````,J``)@`````,`````````"`````@````)````#*@`"8 M`````#``````````@````(````"0````RH``F``````P`````````(````"` M````D````,J``)@`````,`````````"`````@````)````#*@`"8`````#`` M````````@````(````"0````RH``F``````P`````````(````"`````D``` M`,J``)@`````,`````````"`````@````)````#*@`"8`````#`````````` M@````(````"0````RH``F``````P`````````(````"`````D````,J``)@` M````,`````````"`````@````)````#*@`"8`````#``````````@````(`` M``"0````RH``F``````P`````````(````"`````D````,J``)@`````,``` M``````"`````@````)````#*@`"8`````#``````````@````(````"0```` MRH``F``````P`````````(````"`````D````,J``)@`````,`````````"` M````@````)````#*@`"8`````#``````````@````(````"0````RH``F``` M```P`````````(````"`````D````,J``)@`````,`````````"`````@``` M`)````#*@`"8`````#``````````@````(````"0````RH``F``````P```` M`````(````"`````D````,J``)@`````,`````````"`````@````)````#* M@`"8`````#``````````@````(````"0````RH``F``````P`````````(`` M``"`````D````,J``)@`````,`````````"`````@````-@``,"N@`"8```` M`#``````````@````(````"0````RH``F``````P`````````(````"````` MD````,J``)@`````,`````````"`````@````)````#*@`"8`````#`````` M````@````(````"0````RH``F``````P`````````(````"`````D````,J` M`)@`````,`````````"`````@````)````#*@`"8`````#``````````@``` M`(````"0````RH``F``````P`````````(````"`````D````,J``)@````` M,`````````"`````@````)````#*@`"8`````#``````````@````(````"0 M````RH``F``````P`````````(````"`````D````,J``)@`````,``````` M``"`````@````)````#*@`"8`````#``````````@````(````"0````RH`` MF``````P`````````(````"`````D````,J````````'````%0```$4```!- M````B0```"`!```8`@``5@(``)4"``#&`@``_0(``#\#``!]`P``O`,``/8# M````!```.`0``&P$``":!```T@0``.H$```I!0``7@4``&\%``"J!0``Y`4` M``L&```:!@``3@8``(D&``#(!@``!@<``#4'``!O!P``K@<``+H'``#>!P`` M&P@``$`(``!>"```<0@``"H)```S"0``80D``)P)``#9"0``%0H``$X*``!W M"@``BPH``)L*``#5"@``!`L``",+```V"P``5@L``&P+``"'"P``P`L``.P+ M```I#```8PP``(H,``"?#```V0P``!D-```?#0``20T``'0-``"(#0``O0T` M`.L-```'#@``-PX``$8.``!Z#@``B`X``+4.``#&#@``W`X```80```;$``` MEA```,T0```*$0``*A$``%T1``"9$0``IQ$``+X1``#2$0``\!$```\2```Q M$@``7A(``((2``"M$@``PQ(``/`2```6$P``+A,``(H3``"A$P``MA,``-H3 M```(%```(Q0``$\4``""%```GQ0``,<4``#K%```&14``$H5``!R%0``E14` M`+D5``#E%0``$A8``#D6``!A%@``B18``*\6``#0%@``[A8``!D7```Y%P`` M61<``(T7``"U%P``W!<``/D7```?&```3A@``&@8``")&```JA@``,H8``#J M&```#AD``#\9``!J&0``CAD``,`9``#?&0``_QD``"(:``!)&@``81H``(L: M``"Q&@``SQH``.H:``!,*0``4"D``#@`D)EW,````-`````````&``````#_ MOP$`@`$X`)"9=S````#0````````!@``````_[\!`(`!.@"0F7```:(P``BB<``&TK``!.+P``&P```!T````> M````(````"$````C````)0```"8````H``````8``$XO```<``````````H! M```0`0``WP,``.4#``#&!```R00``$`(``!="```7@@``&`(``!B"```<`@` M`"P)```R"0``90D``'$)``#C"0``YPD``',*``!U"@``=PH``(8*``#5"@`` MW0H``/4*``#]"@``;@L``'8+``!2#```6PP``*,,``"L#```"`X```P.``!' M#@``30X``%X.``!D#@``H`X``*4.``"_#@``Q0X``-(1``#6$0``W1$``.(1 M``#H$0``[Q$```<2```,$@``)A(``"L2``!($@``2A(``$T2``!2$@``7A(` M`&02``"9$@``GA(``*T2``"S$@``\!(``/<2```6$P``&Q,``!P3```A$P`` M-Q,``#T3```^$P``1!,``*83``"J$P``P!,``,D3``#:$P``X1,``/43```` M%```"!0```X4```C%```+!0``$\4``!8%```@A0``(D4``#'%```SA0``#L5 M``!!%0``0Q4``$D5``!+%0``414``)85``">%0``GQ4``*,5``"Z%0``OA4` M`+\5``##%0``YA4``/$5``#R%0``]A4``!,6```;%@``'!8``"`6``!!%@`` M118``&D6``!M%@``BA8``)$6``"P%@``N18``-$6``#8%@``&A<``!T7```Z M%P``01<``'`7``!V%P``>!<``($7``"#%P``C!<``(X7``"6%P``MA<``,$7 M``#=%P``XQ<``/H7```"&```(!@``"@8```I&```+1@``"X8```V&```3Q@` M`%,8``!I&```<1@``(H8``"0&```RQ@``-(8``#K&```]!@```\9```3&0`` M%!D``!@9```D&0``*AD``#89```^&0``0!D``$89``"/&0``EQD``,L9``#5 M&0``UQD``-X9``#@&0``Z!D````:```*&@``(QH``"X:``!*&@``4!H``&(: M``!J&@``:QH``&\:``"I&@``L!H``+(:``"Y&@``NAH``+X:``#0&@``UAH` M`.L:``#T&@``#!L``!,;```I&P``,!L``$8;``!-&P``;!L``'(;``",&P`` ME!L``'@=``!^'0```1X```0>```Y'@``/!X``$<>``!1'@``7QX``&0>``!R M'@``=QX``,H>``#5'@``UAX``-@>``#:'@``Y!X```(?```*'P``)1\``"L? M``!3'P``7!\``%T?``!C'P``9!\``&T?``"2'P``FQ\``)P?``"E'P``YA\` M`.T?```2(```'2```$(@``!,(```;2```',@``"4(```G"```,8@``#-(``` M22$``$XA``#?(0``Y2$``.8A``#P(0``\2$``/@A```7(@``(2(``$4B``!, M(@``32(``%DB``!:(@``82(``*LB``"P(@``O2(``,$B``#-(@``TB(``-XB M``#A(@``"2,``!`C``!I(P``<",``'(C``![(P``?",``'\C``"1(P``F",` M`)HC``"C(P``QB,``,TC``#>(P``XB,``.,C``#J(P``!R0```LD```,)``` M$R0``"R0``-4D``#;)```W"0``.`D``#U M)```_"0``!0E```;)0``/"4``$HE``!M)0``="4``'8E``!_)0``D24``)LE M``"<)0``I"4``*4E``"Q)0``R"4``,HE``#=)0``Y"4```(F```))@``"R8` M`!,F```H)@``,"8``'@F``"')@``B28``)`F``"C)@``K28``+TF``##)@`` MW"8``.0F``!")P``2"<``.@X``'P.``")#@``CPX``+4.``"[#@``V`X``-L.``!]#P`` MA`\``&T0``!Y$```S1```-$0```*$0``%!$``%T1``!B$0``F1$``*`1``#2 M$0``UA$``/`1``#W$0``#Q(``!02```Q$@``-A(``$@2``!*$@``31(``%(2 M``!>$@``9!(``((2``"($@``F1(``)X2``"M$@``LQ(``,,2``#)$@``\!(` M`/<2```6$P``&Q,``"X3```V$P``BA,``)(3``"A$P``I1,``+83``"_$P`` MVA,``.$3```(%```#A0``",4```L%```3Q0``%@4``""%```B10``)\4``"D M%```QQ0``,X4``!#%0``214``$L5``!1%0````!?'@``9!X``-H>``#D'@```A\```H?```E'P``*Q\` M`%T?``!C'P``DA\``)L?``#1'P``TQ\``.8?``#M'P``$B```!T@``!"(``` M3"```&T@``!S(```E"```)P@``#&(```S2```/,@``#[(```."$``#XA``!B M(0``9R$``(HA``"3(0``MB$``+TA``#?(0``Y2$``.8A``#P(0``\2$``/@A M```7(@``(2(``$4B``!,(@``FB(``)XB``"](@``P2(``-XB``#A(@``"2,` M`!`C``!#(P``2",``&DC``!P(P``D2,``)@C``#&(P``S2,``.,C``#J(P`` M#"0``!,D```G)```+20``&PD``!O)```CB0``) M````#0```$1A=FED($UA`````@```#,`?4`>````%````$UI M8W)O``$`"H`!@`%__W__`)H```#_@0```````%H`@`````,````` M`$@```!(````$``0``,`!0```!`'2^"H!TOD)```````6@"```````!:`(`` M```#@0````D```"#?_\`````"0```(-__P`````)````@W__`````'H"``!_ M_W___@``!'__`````'__?__]```$?_]__P````!___L``.Y__Q9C&%[W:UI6 MM6U[W5K5K6F,88QAK6F]VM:5K5K6EK6_FM:`F][9SEC&.5__P`````N!```?_]__P````#^?__\ M```*?_\``'__``!__W__`````'__?_\``)I__P````#"`P``?_]__P``_G__ M_@```'___0``"G__``!__W__``!__P````!__P````#N?_\48QAC&$I27O=C M&'.<;WMO>UK67O=6M6UK6_FM:`6][6M;^:UH! M;WM>]_YK6@%O>VM:_'__(F,88QAK6EK6:UI:UFM::UI:UG__:UI:UF][;WM: MUFM:8QAK6F][;WM>]UK6:UIK6F,8;WMG.5K6;WMK6FM:;WMG.6V,8:UIO>VM::UI:UFM::UI6M7__9SGL?_\);WMC&&M:8QAK6F][ M;WMK6FM:7O?^:UH44I1__V,87O=O>V,8:UIO>V][8QAC&%:U?_]O>UK69SE> M]UK6:UIO>VM:^G__``````D```"#?_\`````I1<``'__?_]O>U:U?_]*4DYS M=[UK6FM:1C%"$'.][L?_\";WMK6G.<_E[W M!6]_UK6@-O>VM:4I1K6NQ__P5K6FM:7O=C&&,89SG^;WL9 M8QAO>VM:9SESG%K66M9O>U[W;WM__VM:;WMWO6][7O=:UFVM:7O?C?_\@;WMC&&M:6M9>]UK6:UIO>VM::UI>]V,8 M8QAG.7.<:UIO>VM:7O=K6EK6:UIC&&M:7O=O>V][:UIO>VM:V][5K5G.6M:9SE6M5*4:UIK6E[W2E)O>VM:]G__&U*45K5.]VU[W_FM: M`%*4^'__'6M:]W.<4I1__V,88QAK6FM:7O=C&&,89SEO>V,86M9O>VM: M4I1__UK68QAK6F][7O=G.6M::UIO>_9__P`````)````@W__`````&0```#5 M?_\/:UISG%[W9SEG.6][4I1:UF][9SEO>V][7O=C&&M:7O?^;WL*8QA>]VM: M;WMK6FM:9SEO>V,88QAO>_9__PI6M7>]6M92E&M:6M9O>V][6M96M6M:_E[W MYG__``````D```"#?_\`````J0```/Y__P1"$%[W6M9O>V][W7__"5K69SE> M]V,89SEO>UK68QAK6E:U_6M:%&][5K5G.6][;WM:UF][7O=O>U:U;WMG.6][ M7O=>]VM:;WMO>VM::UISG/M__R-C&&,8:UI>]V][8QA:UFM:6M9C&'.<6M9K M6EK68QAK6E[W;WM:UFM::UIC&&][9SE:UFM::UI:UE[W?_]C&&M:7O=K6EK6 M:UK\?_\`````MP```/Y__PE>]V,87O=K6F_YK6A9>]U[W M:UIO>U[W;WMG.6M:;WMO>V,81C%2E%[W6M9C&&][;WMK6F,89SEK6F]VM:6M9:UE[W9SGC?_\B:UIK6EK6:UI>]V,8;WM>]V]VM:;WMO>VM:7O=G.6,89SEC&&][7O=C&&M:7O=K6F][7O=G.5[W8QAO M>W.<5K5:UOM__P`````)````@W__`````*$```#^?_\>7O=>]VM:;WMC&&M: M;WMK6EK6:UI:UF][6M9K6E*4;WMG.6,8;WMO>U*46M9K6F]V][:UIC&&M:7O=O>V,8:UIK6E:U5K5G.7__:UISG&UK6:UIG.6][;WM:UE[W_F][`6,86M;^ M:UH&;WMK6FM:9SEO>U[W6M;Q?_\B9SESG&M:8QAK6FM:8QA:UE[W:UI>]VM: M7O=K6FM:;WM>]U:U=[UG.6]V][9SEK6F][8QAO>U[W6M9>]UK64I1: MUE[W6M9G.5[W_FM:!5K6:UIO>VZ)__P````"Y````_G__'E[W:UI> M]U:U9SE:UG__:UIK6E[W]V]VM:4I1C&&M:]W__`V,88QAK6F][_FM:&V][:UI2E&M:;WM>]W__5K5K M6FV][7O=O>V][5K5K6FM:6M96M7.<^W__$&M: M:UI>]V,88QAG.6,8;WM>]V]U[W;WM2E&M:;WOI?_\`````"0```(-_ M_P````#3````_G__(&,86M9O>VM:8QAC&&][8QAO>W.<7O=O>U:U9SE:UFM: M8QA:UFUK6:UIO>U[W;WMO>UK67O=K6OE__P]O>U:U:UIC M&&M:;WM:UFM:8QAG.6,89SEC&%K6:UI>]_YK6@I2E'.<7O=K6FM:6M9K6G.< M6M9K6F][_FM:`6][:UK[?_\)8QA2E&][:UIG.5[W4I1:UF,8:UK]7O<0:UIK M6FVM:6M9C&/=__P````"4````U7__ M''.<;WMK6G.<:UIK6E*4=[UK6G.<6M9O>VVM: M:UIO>V,8;WMC&&,8;WO^:UKX?_\B;WMC&%[W:UI:UF][:UIK6F]V][8QA2E'__7O=K6EK6:UIO>V][:UI>]UK6?_]:UE*4?_]K6G__6M9K M6OM__P````!/````_G__%U[W8QAO>V][5K5:UE[W6M9K6F][;WMC&%[W;WM> M]VM:7O=2E&][:UIO>W__9SEG.?UK6@9O>V,8:UIK6F][6M9K6JE__P````"A M````_G__(%[W9SEG.5[W8QAK6E[W;WMO>V]V][6M9K6OE__P!O>_YK6@IO>U:U?_]: MUF][6M9K6DYS?_]K6F][_FM:`F][:UIC&/YK6@)O>UK67O?^:UH!7O=K6OA_ M_PAO>VM:6M9:UE[W9SEK6F,8:UKA?_\`````"0```(-__P````"=````_G__ M'UK67O=:UF,88QAG.6,8;WMO>UK68QAO>UK6:UIO>VM:4I1G.6,88QA>]U[W M:UIO>VM:4I1G.7.<;WM:UFM:7O?X?_\":UIK6EK6_6,8#F]V][4I1S MG%K6:UI6M6M::UIO>U*4?_]>]^Y__P]6M5:U=[U.]VM: M:UIO>U[W9SEK6NA__P````!%````U7__#&M::UI>]V][:UI6M6M:9SEK6FM: M9SEG.6M:Y7__#&,8;WMK6E:U:UIK6F]V][:UIK6F][Y7__`````!<` M``#^?_\$8QAC&&XM__P````"9````_G__(V,8;WMO>V,87O=>]V][ M8QAK6FM:5K5K6G.<4I1:UE[W3G-K6E[W:UIK6F,8;WMC&&][:UIC&&M::UIG M.5[W9SEK6F,8;WMO>_Q__P)6M5:U2E+^5K4%9SEO>VW.<9SEK6E[W7O=K6FM:7O=G.6]U[WZW__``````D` M``"#?_\`````OP```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````"Q````_G__!V,8 M4I1SG&,8;WMK6G.<7O?^:UH`;WO^7O<4;WMG.7__7O=C&&][:UIC&&M:9SE> M]V][:UIG.6,87O=O>VV][_'__$G.<5K5K6FV][:UIK6F,8 M;WMG.5K6;WMG.5*4:UIK6F][ZW__&&M:7O=:UF][:UI>]V,8;WMG.6][:UIO M>W.<9SEK6E[W7O=SG%K6W>]\7__``````D```"#?_\````` MAP```/Y__PEG.6M:7O=K6FM:;WMK6F,8:UI6M?YO>Q5:UDYS?_]K6E:U8QAO M>VM:;WMO>V,85K5O>VM:9SE>]VM:7O=C&&][:UIO>_M__PMO>V][8QA:UFM: MV,8:UI:UFM:7O?D?_\*6M9K6E*4?_]K6F][6M9K6F][8QAK6N-__P`` M```)````@W__`````+,```#^?_\:;WMK6FM:7O=C&&M:8QAC&&][7O=O>V][ M8QAO>U:U:UI>]W.<7O=O>VM::UIO>TYS9SEK6E[W_FM:!&]:UIG.5[W:UI2E&VM:UK6:UI: MUFM::UIO>_-__P````##````_G__(6M::UIG.5[W:UI:UFM:7O=>]V][8QA> M]VM:5K5K6F][6M9:UG__:UI2E%:U3G-K6E[W;WMC&&][4I1:UFM::UIG.6][ M^G__'VVM:6M9K6F][;WMC&&][3G-K6EK68QAK6F][:UIC M&&][9SE:UF][9SEG.6,8;WMC&&M:9SGX?_\#7O=K6FM:9SG^:UH.;WM:UF][ M:UIK6F,8;WMO>VM:]V][[G__``````D```"#?_\`````;0`` M`/Y__P5>]V][6M9K6EK6;WO>?_\.9SEK6FVU[W_FM:!U*4:UI:UG.<3G-__V][ M:UKZ?_\':UIK6F,8:UI>]VM::UI6M?UK6@=6M6M:4I1K6E:UTI27O=C&%[W:UIG.5:U_'__`````$L```#^?_\%8QAC M&$I25K5.UK6:UIO>VM:9SEC&&][6M9K6FM: M7O=G.6M:9SEK6E*4:UJF?_\`````>0```/Y__QU:UFM::UIG.5*4:UIC&%K6 M7O=SG&][:UIO>U*47O=>]V][:UIK6FVM:8QAK6E[W:UIO>V,8;WOV M?_\#8QAK6FM:;WO]VM::UI>]VM::UI>]VM: M;WOI?_\`````"0```(-__P````"@````_G__#EK6:UI*4G__;WM:UFM:;WMK M6FW.<5K5G.?YK6@=>]V,8:UIO>V][8QA>]V][\G__('.<7O=K6EK6 M;WM>]V,8:UI:UG__:UISG&M:;WM.]VM:7O=C&&M:6M9> M]V,8VM:8QAK6OE___YK6@EC&&][4I1K6E[W8QA__V][8QAK6N5__P`` M``!3````U7__%F][8QA>]V][6M9K6EK6;WM__V][4I1:UF][:UI:UF,8:UIK M6F][8QA6M7.<;WOO?_\$:UI>]VM:8QAO>_YK6@):UG__7O?C?_\`````2P`` M`/Y__P5C&&,82E)6M4YS5K7^7O<66M9G.7.<7O=O>V,8:UIG.6M:;WMK6EK6 M6M9K6G.<6M9K6EK6:UI*4FZ9__P````!L````_G__#%K6:UIK6F]W.<;WMK6E[WY7__#&VM:Y7___FM:"E:U9SEG.6][:UIO>UK6:UI__UK6;WO^:UH"6M9K6F][['__ M``````D```"#?_\`````U0```/Y__R-C&&][:UIG.6][:UI:UF][;WM:UE[W M;WM:UF][6M9K6FM:9SEK6F][:UI:UFM:9SEK6E[W3G-SG&M:;WM>]U:U;WM_ M_U[W:UK\?_\38QAC&&M:8QAK6EK66M9K6G.<:UI2E%:U3G-6M5[W4I1SG&M: M;WM.<_YO>PQK6E:U6M9K6F_Q__Q!G.6,8:UI2 ME'__7O=:UF][:UIO>U:U:UIK6G.<:UIK6E[W_FM:!5[W:UIK6E*4:UIO>_)_ M_P````!U````U7__`F][7O=G.?YK6AM:UE:U]VM:;WM>]VM::UI>]VM:4I1>]V,8Z7__`````$<```#^?_\<:UI: MUF,89SEC&&M:8QA:UFU:U5K5WO4(0 M5K56M>1___YK6@!O>]Q__PMK6FM:8QA2E&M::UI:UFM:3G-K6FM:;WO^:UH) M;WMK6F,8:UIK6F,8?_]K6E*4;WOQ?_\`````"0```(-__P````"_````_G__ M(U*45K5.VM:3G-__VM:;WMO>U[W9SE>]VV][8QA>]V][ M;WMK6E:U:UIC&&][8QAK6F]_Q__P5SG%*46M9>]W.<8QC^ M;WL&:UI:UE*49SE__VM:6M;^:UH$6M9K6F][6M9K6O!__PAK6FM:8QA2E&M: M:UI:UFM:3G/^:UH%V,8;WMK6E[W_FM:!U[W:UIK6E[W7O=C&&M:;WOU M?_\`````J@```/Y__R)6M5K6?_]:UFM:7O=>]V][8QA>]VM:5K5K6G__4I12 ME&][:U]>_V]_7O]O?VM?9S]O?VM?8Q]C'U:_3G]6OTY_5K]>_U[_^W__&&M: M8QAO>VU[W;WMC&&M:?_]2E&][8QAG.6M:4I1G.6M:W.<7O=O M>V][\7___FM:#%K65K5K6FM:4I1O>VM:;WM>]V,8;WMC&&M:Z'__``````D` M``"#?_\`````BP```/Y__P)6M5:U2E+^5K437O=G.5[W6M9K6E[W8Q]>_W__ M7O]__V<_9S]K7UK?8Q]K7U[_^)__Q=O>V][6M9>]VM::UI>]VM:6M9K6F][6M9K6G.<;WMG.6M:6M9O>U:U M;WMO>VM:;WOP?_\`````"0```(-__P````"0````_G__!TYS4I1G.5K6;WM6 MM5:U2E+^5K7C?_\1V,8:UIS MG%K6_FM:"5K6:UI>]VM:;WM.U[W9SE>]VM: M;WMK6F][9SE>]VW.<;WMK6EK6[G__`````+<```#^?_\> M8QAK6E*45K5.VV,89SEK6E[W:UIK6E[W:UIC M&&M:8QA6M7__6M9__UK6:UKW?_\-V][:UI:UFM: M9SEK6OY>]P=:UF][?_]O>U[W9SEC&&M:\7__&5[W:UIK6EK6:UI:UF][;WMC M&%K6:UIO>V,8:UIK6F]VM::UI:UFM:7O?R?_\`````"0`` M`(-__P````!S````_G__(&][4I1:UF][:UI:UF,8:UI2E&][;WMC&&M:8QAO M>V]VM:;WM:UF][6M9O>V][8QA:UFM:8QAK6OE__P]G.5*4 M?_]K6E[W8QA:UG__:UI:UF][;WM6M6M:;WMC&+]__P`````)````@W__```` M`(L```#^?_\B5K5>]U*43G-__V][6M9O>UK6:UIO>V]V][5K5SG&M: M:UIO>U[W9SEK6E[W:UIO>VM:7O=:UFM:7O=G.7__8QAK6OM__QESG&M:5K5_ M_V,8;WM.]VM::UI:UFM: MR7__`````&D```#^?_\C6M9K6FM:;WM.U*46M9O>UK6:UIC&&M:;WMK6FM:9SEC&&][_'__ M`&][_FM:!&][5K5__VM:;WNX?_\`````"0```(-__P````!_````_G__&5K6 M:UI:UE[WV M]V][7O?R?_\<VM:;WMK6F][7O=O>UK6:UIK6DI2 M?_]>]V][8QAK6E[W8QAO>U[W;WMG.]V][ M8QAK6K5__P````!1````_G__(6,8:UIC&%[W:UI2E%:U3G-6M5[W7O=K6F,8 M;WMG.5K6VM:;WM2E%[W:UIK6FTI2J'__ M`````(D```#^?_\B6M9:UG.<:UIG.5[W7O=SG&][5K5K6EK6:UI>]VM:8QA: MUF][;WMC&&M:]W.<4I1O>V][8QAO>V][]U:U:UIC&/M__QASG$8Q M?_]O>V,86M9K6F,8:UIK6E[W8QA:UF][6M9C&%:U?_]K6EK6:UIG.6][;WM: MULA__P`````)````@W__`````#$```#^?_\&;WMK6FM:7O=.]P1__V][6M9K6F][N7__``````D```"#?_\`````"0```(-__P`` M```)````@W__``````D```"#?_\`````"0```(-__P`````)````@W__```` M``D```"#?_\`````"0```(-__P`````#@0````#_```````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M``````````````````````````#^_P```PH!```````````````````````! M`````M7-U9PN&Q"3EP@`*RSYKC`````<`0``#`````$```!H````#P```'`` M```%````J`````8```"P````$0```+@````7````P`````L```#(````$``` M`-`````3````V````!8```#@````#0```.@````,````^P````(````0)P`` M'@```#````!0;W-T+4=E;F]M:6-S(&%N9"!-;VQE8W5L87(@26YT97)A8W1I M;VYS($-E;G1E<@`#````2`````,````1`````P```-DI```#````!`(+``L` M````````"P`````````+``````````L`````````'A````$````'````14U" M3U-3``P0```"````'@````8```!4:71L90`#`````0`````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M`````````````````````````````0````(````#````!`````4````&```` M!P````@````)````"@````L````,````#0````X````/````$````!$````2 M````$P```!0````5````%@```!<````8````&0```!H````;````'````!T` M```>````'P```"`````A````(@```",````D````)0```"8````G````*``` M`"D````J````*P```"P````M````+@```"\````P````,0```#(````S```` M-````#4````V````-P```#@````Y````.@```/[___\\````/0```#X````_ M````0````$$```!"````0P```$0```!%````1@```$<```!(````20```$H` M``!+````3````$T```!.````3P```%````!1````4@```%,```!4````50`` M`%8```!7````6````%D```!:````6P```%P```!=````7@```%\```!@```` M_O___V(```!C````9````&4```!F````9P```&@```!I````:@```&L```!L M````;0```&X```!O````<````'$```#^____0```/[____]____?````/[____^_____O________]2`&\`;P!T M`"``10!N`'0`<@!Y```````````````````````````````````````````` M````````````````%@`%`?__________`P````8)`@``````P````````$8` M````````````````9VDYBPK(`7X```"``````````#$`5`!A`&(`;`!E```` M```````````````````````````````````````````````````````````` M```````.``(!_____P4```#_____```````````````````````````````` M````````````````.P```-=+````````5P!O`'(`9`!$`&\`8P!U`&T`90!N M`'0``````````````````````````````````````````````````````!H` M`@$!````__________\````````````````````````````````````````` M````````````DG4````````%`%,`=0!M`&T`80!R`'D`20!N`&8`;P!R`&T` M80!T`&D`;P!N````````````````````````````````````*``"`0(````$ M````_____P```````````````````````````````````````````````&$` M``"D(`````````4`1`!O`&,`=0!M`&4`;@!T`%,`=0!M`&T`80!R`'D`20!N M`&8`;P!R`&T`80!T`&D`;P!N```````````````X``(!________________ M````````````````````````````````````````````````<@`````0```` M`````0!#`&\`;0!P`$\`8@!J```````````````````````````````````` M`````````````````````````````!(``@#_______________\````````` M````````````````````````````````````````````6``````````````` M```````````````````````````````````````````````````````````` M`````````````````````````/_______________P`````````````````` M```````````````````````````````````````````````````````````` M```````````````````````````````````````````````````````````` M````````````````________________```````````````````````````` M`````````````````````````````````````0```/[_________________ M____________________________________________________________ M____________________________________________________________ M____________________________________________________________ M____________________________________________________________ M____________________________________________________________ M____________________________________________________________ M____________________________________________________________ M____________________________________________________________ M____________________________________________________________ M____________________________________________________________ M__________________________________________________________\! M`/[_`@`!`/____\&"0(``````,````````!&&````$UI8W)Onew($acdfile) ; my $name = $acd->name or die "No name !"; my $NAME = $name; $NAME =~ s/(.)/\U$1/g; my $purpose = $acd->documentation; my $groups = join(",", $acd->groups); print <<"__XML__"; ]> &dhtitle; &dhproduct; &dhrelease; &dhusername; Wrote the script used to autogenerate this manual page.
&dhemail;
This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package. It can be redistributed under the same terms as EMBOSS itself. &dhucpackage; &dhsection; &dhpackage; $purpose &dhpackage; __XML__ foreach my $parameter ( $acd->param) { next if $$parameter{datatype} =~ /section/; my ($paraname, $argname, $paratype) = ( $$parameter{name}, $$parameter{datatype}, $$parameter{type} ); my $additional = 'choice="plain"'; $additional = 'choice="opt"' if $$parameter{additional} eq 'Y'; print qq(\t\t\t\n); } print <<"__XML__"; &dhpackage; DESCRIPTION &dhpackage; is a command line program from EMBOSS (the European Molecular Biology Open Software Suite). It is part of the "$groups" command group(s). OPTIONS __XML__ foreach my $parameter( $acd->param) { # Does a section begin ? if ($$parameter{datatype} eq "section") { print qq(\t\t\n\t\t\t$$parameter{information}\n\t\t\t\n); next; } # Does a section end ? if ($$parameter{datatype} eq "endsection") { print "\t\t\t\n\t\t\n"; next; } # Is there a Default value ? my $default = ''; $default = " Default value: $$parameter{default}" if $$parameter{default}; # Use entities when necessary: $$parameter{help} =~ s/&/&/g ; $$parameter{help} =~ s//>/g ; $default =~ s/&/&/g ; $default =~ s//>/g ; print<<"__XML__"; $$parameter{datatype} $$parameter{help}$default __XML__ } print<<"__XML__"; BUGS Bugs can be reported to the Debian Bug Tracking system (http://bugs.debian.org/emboss), or directly to the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031). SEE ALSO &dhpackage; is fully documented via the tfm1 system. __XML__ debian/reference0000644000000000000000000000076312214054043011050 0ustar @article{Rice2000276, title = "EMBOSS: The European Molecular Biology Open Software Suite", journal = "Trends in Genetics", volume = "16", number = "6", pages = "276 - 277", year = "2000", note = "", issn = "0168-9525", doi = "DOI: 10.1016/S0168-9525(00)02024-2", url = "http://www.sciencedirect.com/science/article/B6TCY-40CRS27-G/2/b4e5945c07c58d5a1257cbd685971317", author = "Peter Rice and Ian Longden and Alan Bleasby", keywords = "Bioinformatics", keywords = "Database", keywords = "EMBOSS" } debian/README.source0000644000000000000000000000060312214054043011337 0ustar This packages uses a patch system. Please read /usr/share/doc/quilt/README.source for more informations. The binary packages are built against the zlib and expat library distributed in Debian, not the conveniences copies co-distributed with EMBOSS. This is done by: - passing ‘--enable-systemlibs’ to the configure command. - passing ‘LDFLAGS="-lexpat"’ to the make command. debian/emboss-doc.doc-base.emboss-admin0000644000000000000000000000162512214054043015174 0ustar Document: emboss-admin Title: The EMBOSS Administrator’s Guide Author: David Martin, EMBnet Norway Peter Rice, LION Bioscience Alan Bleasby, HGMP (EMBnet UK) Section: Science/Biology Abstract: This guide has been written to assist system administrators and developers with the installation and configuration of EMBOSS. If you are reading this to find out how to do bioinformatics then you are wasting your time. You are referred instead to the Resources chapter below where there is a list of more relevant literature and web sites. Experienced users may find this document useful for configuring their own databases and customising their EMBOSS experience. . This guide relates to EMBOSS 2.5.0 Format: PostScript Files: /usr/share/doc/emboss-doc/doc/manuals/admin.ps Format: PDF Files: /usr/share/doc/emboss-doc/doc/manuals/admin.pdf Format: DVI Files: /usr/share/doc/emboss-doc/doc/manuals/admin.dvi debian/emboss-doc.doc-base.domainatrix0000644000000000000000000000127112214054043015132 0ustar Document: domainatrix Title: Domainatrix guide. Abstract: This document describes the use of EMBOSS applications in the EMBASSY package domainatrix. Most of these directly or indirectly make use of the protein structure databases pdb and scop. All of the applications here were written by Jon Ison, Ranjeeva Ranasinghe, Matt Blades and Waqas Awan and coordinated by Jon Ison to whom enquiries should be sent (email jison@hgmp.mrc.ac.uk). This software is part of an experimental analysis pipeline and we provide it in the hope that it will be useful. Section: Science/Biology Format: Text Files: /usr/share/doc/emboss-doc/doc/manuals/domainatrix.txt debian/emboss-doc.doc-base.emboss-groups0000644000000000000000000000055012214054043015417 0ustar Document: emboss-groups Title: EMBOSS Application Groups Author: The EMBOSS Developpers Section: Science/Biology Abstract: Documentation of the EMBOSS applications organized into logical groups according to their function. Format: HTML Index: /usr/share/doc/emboss-doc/doc/programs/html/groups.html Files: /usr/share/doc/emboss-doc/doc/programs/html/*.html debian/README.debian0000644000000000000000000000355312214054043011270 0ustar EMBOSS for Debian ================= Some programs renamed --------------------- Some programs in EMBOSS have a name which is also used by other programs from other packages. The Debian distribution does not allow two packages to conflict in this way. Therfore 'cons' has been renamed 'em_cons' and 'pscan has been renamed 'em_pscan'. There is a directory in which the program names are guaranteed to be always unchanged, /usr/lib/emboss. You can prepend it to your PATH, with a command such as 'PATH = /usr/lib/emboss:$PATH' with Bourne shells, so that when you run 'cons' or 'pscan', it is always the EMBOSS program. Other programs could be renamed in the future, so it is strongly recommended to use this path in your scripts. tfm uses Debian's pager by default ---------------------------------- The `tfm' program will use /usr/bin/pager instead of /usr/bin/more by default. /usr/bin/pager is managed via the `update-alternatives' utility and can point to other pagers such as `less' and `most'. This can be overridden by using the PAGER environment variable, just as in default EMBOSS installations. EMBOSS Quick Guide relicenced ----------------------------- This package contains a relicenced version of the EMBOSS Quick Guide. Its uuencoded sources (in MS Word format) are included in the Debian source package 'emboss'. Notes about how this package is tested -------------------------------------- The EMBOSS packages for Debian are tested during the build process by running the regression checks of the ‘test/qa/qatest.csh’ script. You can consult the results in the build logs available at ‘http://buildd.debian.org/emboss’. In addition, the packages are tested locally by the developer performing the upload, by running a couple of very simple programs like ‘embossversion’ and ‘tfm’. -- Charles Plessy Fri, 07 Mar 2008 10:23:12 +0900 debian/jemboss.menu0000644000000000000000000000032512214054043011511 0ustar ?package(jemboss):needs="X11" section="Applications/Science/Biology" \ title="Jemboss" \ description="Graphical user interface for the European Molecular Biology Open Software Suite." \ command="runJemboss.sh" debian/emboss-doc.doc-base.emboss-qg0000644000000000000000000000052312214054043014507 0ustar Document: emboss-qg Title: EMBOSS, a quick guide. Author: David Martin, EMBnet Norway Abstract: Summary of emboss programs and their options on a recto-verso page. Section: Science/Biology Format: PostScript Files: /usr/share/doc/emboss-doc/doc/manuals/emboss_qg.ps Format: PDF Files: /usr/share/doc/emboss-doc/doc/manuals/emboss_qg.pdf debian/rules0000755000000000000000000001166012214054043010245 0ustar #!/usr/bin/make -f export DH_VERBOSE=1 %: dh $@ --with autotools-dev,quilt,autoreconf VERSION := $(shell dpkg-parsechangelog | grep Ver | cut -d' ' -f2 | cut -d- -f1) RENAMED := cons pscan EMBOSS-TMP = $(CURDIR)/debian/emboss_tmp EMBOSS = $(CURDIR)/debian/emboss EMBOSS-TEST = $(CURDIR)/debian/emboss-test EMBOSS-LIB = $(CURDIR)/debian/emboss-lib CONFFLAGS = --bindir=/usr/lib/emboss CONFFLAGS += --libdir=/usr/lib/emboss/lib CONFFLAGS += --includedir=/usr/lib/emboss/include CONFFLAGS += --enable-systemlibs CONFFLAGS += --with-java=/usr/lib/jvm/default-java/include CONFFLAGS += --with-javaos=/usr/lib/jvm/default-java/include/linux CPPFLAGS:=$(shell dpkg-buildflags --get CPPFLAGS) CFLAGS:=$(shell dpkg-buildflags --get CFLAGS) DEB_LDFLAGS += -lexpat DEB_LDFLAGS += $(shell mysql_config --libs) DEB_LDFLAGS += -lpq DEB_LDFLAGS += $(shell dpkg-buildflags --get LDFLAGS) #DEB_LDFLAGS += $(shell pg_config | grep LIBS | cut -f2 -d=) override_dh_auto_configure: dh_autotools-dev_updateconfig dh_auto_configure -- $(CONFFLAGS) override_dh_auto_build: dh_auto_build -- AJAX_FIXED_ROOT=\\\"/usr/share/EMBOSS\\\" CPPFLAGS="$(CPPFLAGS)" CFLAGS="$(CFLAGS)" LDFLAGS="$(DEB_LDFLAGS)" override_dh_clean: dh_autotools-dev_restoreconfig rm --force --recursive debian/emboss_tmp find jemboss/ -type f -name "*.class" | xargs -r rm -f [ ! -d debian/testbackup ] || ( $(RM) --recursive test ; mv debian/testbackup test ) dh_clean --exclude=feattext.html~ config.status test-stamp install-stamp override_dh_auto_install-arch: ### Binaries and data go to a temporary dir before being moved to their own package ### $(MAKE) -C emboss install DESTDIR=$(EMBOSS-TMP) # Make symbolic links from /usr/bin to /usr/lib/emboss cd $(EMBOSS)/usr/bin/ ; \ for i in $(EMBOSS-TMP)/usr/lib/emboss/* ; \ do ln -sf ../lib/emboss/`basename $$i` . ; \ done ### Renaming conflicting binaries (see also in binary-arch) ### for i in $(RENAMED) ; \ do mv $(EMBOSS)/usr/bin/$$i $(EMBOSS)/usr/bin/em_$$i ; \ done ### EMBOSS libraries go in the emboss-lib package. ### $(MAKE) -C ajax install DESTDIR=$(EMBOSS-LIB) $(MAKE) -C nucleus install DESTDIR=$(EMBOSS-LIB) $(MAKE) -C plplot install DESTDIR=$(EMBOSS-LIB) find $(EMBOSS-LIB)/usr/lib -name '*.la' -exec rm {} \; ### Documentation goes in emboss-doc. ### $(MAKE) -C doc install DESTDIR=$(CURDIR)/debian/emboss-doc antiword $(CURDIR)/debian/emboss-doc/usr/share/EMBOSS/doc/manuals/domainatrix.doc > $(CURDIR)/debian/emboss-doc/usr/share/EMBOSS/doc/manuals/domainatrix.txt # Remove this file when the relicenced file becomes part of the upstream tarball. uudecode -o $(CURDIR)/debian/emboss-doc/usr/share/EMBOSS/doc/manuals/EMBOSS_qg.pdf $(CURDIR)/debian/EMBOSS_qg_new.pdf.uu override_dh_auto_install-indep: $(MAKE) -C jemboss install DESTDIR=$(CURDIR)/debian/jemboss bindir=/usr/bin # install target seems to remove executable flag which is claimed by lintian find $(CURDIR)/debian/jemboss/usr/share/EMBOSS/jemboss/utils -type f -not -executable -name "*sh" -exec chmod a+x \{\} \; # dangling LICEN[CS]E FILE rm $(CURDIR)/debian/jemboss/usr/share/EMBOSS/jemboss/LICENSE ### Installation of the test suite cp -a test $(CURDIR)/debian/emboss-test/usr/share/EMBOSS/ sed -i "/SET emboss_tempdata/cSET emboss_tempdata /usr/share/EMBOSS/test" $(CURDIR)/debian/emboss-test/usr/share/EMBOSS/test/.embossrc sed -i "/SET emboss_qadata/cSET emboss_qadata /usr/share/EMBOSS/test" $(CURDIR)/debian/emboss-test/usr/share/EMBOSS/test/.embossrc mv $(CURDIR)/debian/emboss-test/usr/share/EMBOSS/test/.embossrc $(CURDIR)/debian/emboss-test/etc/emboss/embossrc.d/emboss-test find $(CURDIR)/debian/emboss-test/usr/share/EMBOSS/test/data -executable -type f -exec chmod a-x \{\} \; find $(CURDIR)/debian/emboss-test/usr/share/EMBOSS/test -type d -name CVS | xargs rm -rf find $(CURDIR)/debian/emboss-test/usr/share/EMBOSS/test -type f -name .cvsignore -delete override_dh_auto_test: $(RM) test-stamp [ -d debian/testbackup ] || cp -a test debian/testbackup sed -i "/SET emboss_tempdata/cSET emboss_tempdata $(CURDIR)/test" test/.embossrc sed -i "/SET emboss_qadata/cSET emboss_qadata $(CURDIR)/test" test/.embossrc echo "SET emboss_acdroot $(CURDIR)/emboss/acd" >> test/.embossrc echo "SET emboss_data $(CURDIR)/emboss/data" >> test/.embossrc echo "SET emboss_docroot $(CURDIR)/doc" >> test/.embossrc cd test/qa && LS_COLORS='' EMBOSSRC=$(CURDIR)/test PATH=$(CURDIR)/emboss:$$PATH EMBOSS_ROOT=../../../ ./qatest.csh override_dh_installchangelogs: dh_installchangelogs -k ChangeLog override_dh_installman: dh_installman -a -p emboss for i in $(RENAMED) ; \ do dh_link usr/share/man/man1/$$i.1e.gz usr/share/man/man1/em_$$i.1e.gz ; \ done override_dh_builddeb: dh_builddeb -- -Z xz # Target to refresh the manpages; needs libemboss-acd-perl, xsltproc, docbook-xml and docbook-xsl manpages: debian/manpages/success debian/manpages/success: debian/build-manpages.sh echo "The manpages have been sucessfully built" > debian/manpages/success debian/emboss-lib.lintian-overrides0000644000000000000000000000105112214054043014572 0ustar # EMBOSS unfortunately uses a modified copy of the PCRE library. Upstream # understands the problems it causes for us, but will not remove it in the # short term. The other embedded and modified library is PLplot. Thanks # to Upstream's efforts, the emboss packages in Debian can be built # against Debian's zlib and expat libraries instead of the convenience code # copies in the original upstream sources. # -- Charles Plessy Thu, 16 Sep 2010 20:27:09 +0900 emboss-lib: embedded-library usr/lib/emboss/lib/libepcre.so.7.0.9: pcre3debian/manpages/0000755000000000000000000000000012214054043010754 5ustar debian/manpages/entrailshtml.1e0000644000000000000000000000477712214054043013730 0ustar '\" t .\" Title: ENTRAILSHTML .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ENTRAILSHTML" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" entrailshtml \- Reports the internal structures in HTML .SH "SYNOPSIS" .HP \w'\fBentrailshtml\fR\ 'u \fBentrailshtml\fR \fB\-tables\ \fR\fB\fIlist\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBentrailshtml\fR\ 'u \fBentrailshtml\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBentrailshtml\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Misc" command group(s)\&. .SH "OPTIONS" .SS "required section" .PP \fB\-tables\fR \fIlist\fR .RS 4 Default value: all .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP entrailshtml is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/entrygo.1e0000644000000000000000000000514312214054043012675 0ustar '\" t .\" Title: ENTRYGO .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ENTRYGO" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" entrygo \- Identify and retrieve sequence entries containing GO terms .SH "SYNOPSIS" .HP \w'\fBentrygo\fR\ 'u \fBentrygo\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-term\ \fR\fB\fIstring\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBentrygo\fR\ 'u \fBentrygo\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBentrygo\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-term\fR \fIstring\fR .RS 4 .RE .SS "Required section" .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP entrygo is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/dbxcompress.1e0000644000000000000000000000530012214054043013532 0ustar '\" t .\" Title: DBXCOMPRESS .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DBXCOMPRESS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" dbxcompress \- Compress an uncompressed dbx index .SH "SYNOPSIS" .HP \w'\fBdbxcompress\fR\ 'u \fBdbxcompress\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-field\ \fR\fB\fIstring\fR\fR \fB\-indexdir\ \fR\fB\fIdirectory\fR\fR \fB\-$(dbname)\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBdbxcompress\fR\ 'u \fBdbxcompress\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdbxcompress\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-dbname\fR \fIstring\fR .RS 4 .RE .PP \fB\-field\fR \fIstring\fR .RS 4 .RE .PP \fB\-indexdir\fR \fIdirectory\fR .RS 4 .RE .SS "Required section" .SS "Advanced section" .SS "Output section" .PP \fB\-$(dbname)\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP dbxcompress is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/newcpgseek.1e0000644000000000000000000000516612214054043013346 0ustar '\" t .\" Title: NEWCPGSEEK .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "NEWCPGSEEK" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" newcpgseek \- Identify and report CpG\-rich regions in nucleotide sequence(s) .SH "SYNOPSIS" .HP \w'\fBnewcpgseek\fR\ 'u \fBnewcpgseek\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-score\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBnewcpgseek\fR\ 'u \fBnewcpgseek\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBnewcpgseek\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:CpG Islands" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Required section" .PP \fB\-score\fR \fIinteger\fR .RS 4 Default value: 17 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP newcpgseek is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/backtranambig.1e0000644000000000000000000000523112214054043013771 0ustar '\" t .\" Title: BACKTRANAMBIG .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "BACKTRANAMBIG" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" backtranambig \- Back\-translate a protein sequence to ambiguous nucleotide sequence .SH "SYNOPSIS" .HP \w'\fBbacktranambig\fR\ 'u \fBbacktranambig\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-table\ \fR\fB\fIlist\fR\fR] \fB\-outfile\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBbacktranambig\fR\ 'u \fBbacktranambig\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBbacktranambig\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Translation,Protein:Composition" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Additional section" .PP \fB\-table\fR \fIlist\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP backtranambig is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/revseq.1e0000644000000000000000000000545612214054043012522 0ustar '\" t .\" Title: REVSEQ .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "REVSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" revseq \- Reverse and complement a nucleotide sequence .SH "SYNOPSIS" .HP \w'\fBrevseq\fR\ 'u \fBrevseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-reverse\ \fR\fB\fIboolean\fR\fR \fB\-complement\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBrevseq\fR\ 'u \fBrevseq\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBrevseq\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Advanced section" .PP \fB\-reverse\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to reverse the output sequence Default value: Y .RE .PP \fB\-complement\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to complement the output sequence Default value: Y .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP revseq is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/acdpretty.1e0000644000000000000000000000444012214054043013204 0ustar '\" t .\" Title: ACDPRETTY .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ACDPRETTY" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" acdpretty \- Correctly reformat an application ACD file .SH "SYNOPSIS" .HP \w'\fBacdpretty\fR\ 'u \fBacdpretty\fR .HP \w'\fBacdpretty\fR\ 'u \fBacdpretty\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBacdpretty\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Acd,Data retrieval:Tool data" command group(s)\&. .SH "OPTIONS" .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP acdpretty is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/antigenic.1e0000644000000000000000000000511112214054043013142 0ustar '\" t .\" Title: ANTIGENIC .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ANTIGENIC" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" antigenic \- Finds antigenic sites in proteins .SH "SYNOPSIS" .HP \w'\fBantigenic\fR\ 'u \fBantigenic\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-minlen\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR .HP \w'\fBantigenic\fR\ 'u \fBantigenic\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBantigenic\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Motifs" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Required section" .PP \fB\-minlen\fR \fIinteger\fR .RS 4 Default value: 6 .RE .SS "Output section" .PP \fB\-outfile\fR \fIreport\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP antigenic is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/domtestc.1e0000644000000000000000000000454012214054043013030 0ustar '\" t .\" Title: DOMTESTC .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DOMTESTC" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" domtestc \- Create and write out some typical XML .SH "SYNOPSIS" .HP \w'\fBdomtestc\fR\ 'u \fBdomtestc\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBdomtestc\fR\ 'u \fBdomtestc\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdomtestc\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP domtestc is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/seqmatchall.1e0000644000000000000000000000516012214054043013503 0ustar '\" t .\" Title: SEQMATCHALL .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SEQMATCHALL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" seqmatchall \- All\-against\-all word comparison of a sequence set .SH "SYNOPSIS" .HP \w'\fBseqmatchall\fR\ 'u \fBseqmatchall\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR \fB\-wordsize\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIalign\fR\fR .HP \w'\fBseqmatchall\fR\ 'u \fBseqmatchall\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBseqmatchall\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Local" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqset\fR .RS 4 .RE .SS "Required section" .PP \fB\-wordsize\fR \fIinteger\fR .RS 4 Default value: 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIalign\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP seqmatchall is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/pscan.1e0000644000000000000000000000524312214054043012313 0ustar '\" t .\" Title: PSCAN .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PSCAN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" pscan \- Scans protein sequence(s) with fingerprints from the PRINTS database .SH "SYNOPSIS" .HP \w'\fBpscan\fR\ 'u \fBpscan\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-emin\ \fR\fB\fIinteger\fR\fR \fB\-emax\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBpscan\fR\ 'u \fBpscan\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBpscan\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Motifs" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Required section" .PP \fB\-emin\fR \fIinteger\fR .RS 4 Default value: 2 .RE .PP \fB\-emax\fR \fIinteger\fR .RS 4 Default value: 20 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP pscan is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/martregistry.1e0000644000000000000000000000532112214054043013740 0ustar '\" t .\" Title: MARTREGISTRY .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "MARTREGISTRY" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" martregistry \- Show Biomart registries listed on a host .SH "SYNOPSIS" .HP \w'\fBmartregistry\fR\ 'u \fBmartregistry\fR \fB\-host\ \fR\fB\fIstring\fR\fR \fB\-path\ \fR\fB\fIstring\fR\fR \fB\-port\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBmartregistry\fR\ 'u \fBmartregistry\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBmartregistry\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-host\fR \fIstring\fR .RS 4 Default value: www\&.biomart\&.org .RE .PP \fB\-path\fR \fIstring\fR .RS 4 Default value: /biomart/martservice .RE .PP \fB\-port\fR \fIinteger\fR .RS 4 Default value: 80 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP martregistry is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/remap.1e0000644000000000000000000002461612214054043012320 0ustar '\" t .\" Title: REMAP .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "REMAP" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" remap \- Display restriction enzyme binding sites in a nucleotide sequence .SH "SYNOPSIS" .HP \w'\fBremap\fR\ 'u \fBremap\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-mfile\ \fR\fB\fIdatafile\fR\fR \fB\-enzymes\ \fR\fB\fIstring\fR\fR \fB\-sitelen\ \fR\fB\fIinteger\fR\fR [\fB\-mincuts\ \fR\fB\fIinteger\fR\fR] [\fB\-maxcuts\ \fR\fB\fIinteger\fR\fR] [\fB\-single\ \fR\fB\fIboolean\fR\fR] [\fB\-blunt\ \fR\fB\fIboolean\fR\fR] [\fB\-sticky\ \fR\fB\fIboolean\fR\fR] [\fB\-ambiguity\ \fR\fB\fIboolean\fR\fR] [\fB\-plasmid\ \fR\fB\fIboolean\fR\fR] [\fB\-methylation\ \fR\fB\fIboolean\fR\fR] [\fB\-commercial\ \fR\fB\fIboolean\fR\fR] [\fB\-table\ \fR\fB\fIlist\fR\fR] [\fB\-frame\ \fR\fB\fIlist\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-cutlist\ \fR\fB\fIboolean\fR\fR] [\fB\-flatreformat\ \fR\fB\fIboolean\fR\fR] [\fB\-limit\ \fR\fB\fIboolean\fR\fR] \fB\-translation\ \fR\fB\fIboolean\fR\fR \fB\-reverse\ \fR\fB\fIboolean\fR\fR \fB\-orfminsize\ \fR\fB\fIinteger\fR\fR \fB\-uppercase\ \fR\fB\fIrange\fR\fR \fB\-highlight\ \fR\fB\fIrange\fR\fR \fB\-threeletter\ \fR\fB\fIboolean\fR\fR \fB\-number\ \fR\fB\fIboolean\fR\fR \fB\-width\ \fR\fB\fIinteger\fR\fR \fB\-length\ \fR\fB\fIinteger\fR\fR \fB\-margin\ \fR\fB\fIinteger\fR\fR \fB\-name\ \fR\fB\fIboolean\fR\fR \fB\-description\ \fR\fB\fIboolean\fR\fR \fB\-offset\ \fR\fB\fIinteger\fR\fR \fB\-html\ \fR\fB\fIboolean\fR\fR .HP \w'\fBremap\fR\ 'u \fBremap\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBremap\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Display,Nucleic:Restriction,Nucleic:Translation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-mfile\fR \fIdatafile\fR .RS 4 Default value: Emethylsites\&.dat .RE .SS "Required section" .PP \fB\-enzymes\fR \fIstring\fR .RS 4 The name \*(Aqall\*(Aq reads in all enzyme names from the REBASE database\&. You can specify enzymes by giving their names with commas between then, such as: \*(AqHincII,hinfI,ppiI,hindiii\*(Aq\&. The case of the names is not important\&. You can specify a file of enzyme names to read in by giving the name of the file holding the enzyme names with a \*(Aq@\*(Aq character in front of it, for example, \*(Aq@enz\&.list\*(Aq\&. Blank lines and lines starting with a hash character or \*(Aq!\*(Aq are ignored and all other lines are concatenated together with a comma character \*(Aq,\*(Aq and then treated as the list of enzymes to search for\&. An example of a file of enzyme names is: ! my enzymes HincII, ppiII ! other enzymes hindiii HinfI PpiI Default value: all .RE .PP \fB\-sitelen\fR \fIinteger\fR .RS 4 This sets the minimum length of the restriction enzyme recognition site\&. Any enzymes with sites shorter than this will be ignored\&. Default value: 4 .RE .SS "Additional section" .PP \fB\-mincuts\fR \fIinteger\fR .RS 4 This sets the minimum number of cuts for any restriction enzyme that will be considered\&. Any enzymes that cut fewer times than this will be ignored\&. Default value: 1 .RE .PP \fB\-maxcuts\fR \fIinteger\fR .RS 4 This sets the maximum number of cuts for any restriction enzyme that will be considered\&. Any enzymes that cut more times than this will be ignored\&. Default value: 2000000000 .RE .PP \fB\-single\fR \fIboolean\fR .RS 4 If this is set then this forces the values of the mincuts and maxcuts qualifiers to both be 1\&. Any other value you may have set them to will be ignored\&. Default value: N .RE .PP \fB\-blunt\fR \fIboolean\fR .RS 4 This allows those enzymes which cut at the same position on the forward and reverse strands to be considered\&. Default value: Y .RE .PP \fB\-sticky\fR \fIboolean\fR .RS 4 This allows those enzymes which cut at different positions on the forward and reverse strands, leaving an overhang, to be considered\&. Default value: Y .RE .PP \fB\-ambiguity\fR \fIboolean\fR .RS 4 This allows those enzymes which have one or more \*(AqN\*(Aq ambiguity codes in their pattern to be considered Default value: Y .RE .PP \fB\-plasmid\fR \fIboolean\fR .RS 4 If this is set then this allows searches for restriction enzyme recognition site and cut positions that span the end of the sequence to be considered\&. Default value: N .RE .PP \fB\-methylation\fR \fIboolean\fR .RS 4 If this is set then RE recognition sites will not match methylated bases\&. Default value: N .RE .PP \fB\-commercial\fR \fIboolean\fR .RS 4 If this is set, then only those enzymes with a commercial supplier will be searched for\&. This qualifier is ignored if you have specified an explicit list of enzymes to search for, rather than searching through \*(Aqall\*(Aq the enzymes in the REBASE database\&. It is assumed that, if you are asking for an explicit enzyme, then you probably know where to get it from and so all enzymes names that you have asked to be searched for, and which cut, will be reported whether or not they have a commercial supplier\&. Default value: Y .RE .PP \fB\-table\fR \fIlist\fR .RS 4 .RE .PP \fB\-frame\fR \fIlist\fR .RS 4 This allows you to specify the frames that are translated\&. If you are not displaying cut sites on the reverse sense, then the reverse sense translations will not be displayed even if you have requested frames 4, 5 or 6\&. By default, all six frames will be displayed\&. Default value: 6 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-cutlist\fR \fIboolean\fR .RS 4 This produces lists in the output of the enzymes that cut, those that cut but are excluded because that cut fewer times than mincut or more times than maxcut and those enzymes that do not cut\&. Default value: Y .RE .PP \fB\-flatreformat\fR \fIboolean\fR .RS 4 This changes the output format to one where the recognition site is indicated by a row of \*(Aq===\*(Aq characters and the cut site is pointed to by a \*(Aq>\*(Aq character in the forward sense, or a \*(Aq<\*(Aq in the reverse sense strand\&. Default value: N .RE .PP \fB\-limit\fR \fIboolean\fR .RS 4 This limits the reporting of enzymes to just one enzyme from each group of isoschizomers\&. The enzyme chosen to represent an isoschizomer group is the prototype indicated in the data file \*(Aqembossre\&.equ\*(Aq, which is created by the program \*(Aqrebaseextract\*(Aq\&. If you prefer different prototypes to be used, make a copy of embossre\&.equ in your home directory and edit it\&. If this value is set to be false then all of the input enzymes will be reported\&. You might like to set this to false if you are supplying an explicit set of enzymes rather than searching \*(Aqall\*(Aq of them\&. Default value: Y .RE .PP \fB\-translation\fR \fIboolean\fR .RS 4 This displays the 6\-frame translations of the sequence in the output\&. Default value: Y .RE .PP \fB\-reverse\fR \fIboolean\fR .RS 4 This displays the cut sites and translation of the reverse sense\&. Default value: Y .RE .PP \fB\-orfminsize\fR \fIinteger\fR .RS 4 This sets the minimum size of Open Reading Frames (ORFs) to display in the translations\&. All other translation regions are masked by changing the amino acids to \*(Aq\-\*(Aq characters\&. .RE .PP \fB\-uppercase\fR \fIrange\fR .RS 4 Regions to put in uppercase\&. If this is left blank, then the sequence case is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 24\-45, 56\-78 1:45, 67=99;765\&.\&.888 1,5,8,10,23,45,57,99 .RE .PP \fB\-highlight\fR \fIrange\fR .RS 4 Regions to colour if formatting for HTML\&. If this is left blank, then the sequence is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are followed by any valid HTML font colour\&. Examples of region specifications are: 24\-45 blue 56\-78 orange 1\-100 green 120\-156 red A file of ranges to colour (one range per line) can be specified as \*(Aq@filename\*(Aq\&. .RE .PP \fB\-threeletter\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-number\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-width\fR \fIinteger\fR .RS 4 Default value: 60 .RE .PP \fB\-length\fR \fIinteger\fR .RS 4 .RE .PP \fB\-margin\fR \fIinteger\fR .RS 4 Default value: 10 .RE .PP \fB\-name\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to display the ID name of the sequence Default value: Y .RE .PP \fB\-description\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to display the description of the sequence Default value: Y .RE .PP \fB\-offset\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-html\fR \fIboolean\fR .RS 4 Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP remap is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/textvalid.1e0000644000000000000000000000535212214054043013214 0ustar '\" t .\" Title: TEXTVALID .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "TEXTVALID" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" textvalid \- Check a plain text format is valid .SH "SYNOPSIS" .HP \w'\fBtextvalid\fR\ 'u \fBtextvalid\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR [\fB\-type\ \fR\fB\fIlist\fR\fR] \fB\-logfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBtextvalid\fR\ 'u \fBtextvalid\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBtextvalid\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Misc" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .SS "Required section" .SS "Additional section" .PP \fB\-type\fR \fIlist\fR .RS 4 If you know the type of file content then specify it using this option\&. This will help textvalid to identify and validate the file format\&. .RE .SS "Advanced section" .SS "Output section" .PP \fB\-logfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP textvalid is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/prettyplot.1e0000644000000000000000000001377112214054043013442 0ustar '\" t .\" Title: PRETTYPLOT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PRETTYPLOT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" prettyplot \- Draw a sequence alignment with pretty formatting .SH "SYNOPSIS" .HP \w'\fBprettyplot\fR\ 'u \fBprettyplot\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR [\fB\-matrixfile\ \fR\fB\fImatrix\fR\fR] [\fB\-residuesperline\ \fR\fB\fIinteger\fR\fR] [\fB\-resbreak\ \fR\fB\fIinteger\fR\fR] [\fB\-ccolours\ \fR\fB\fIboolean\fR\fR] [\fB\-cidentity\ \fR\fB\fIstring\fR\fR] [\fB\-csimilarity\ \fR\fB\fIstring\fR\fR] [\fB\-cother\ \fR\fB\fIstring\fR\fR] [\fB\-docolour\ \fR\fB\fIboolean\fR\fR] [\fB\-shade\ \fR\fB\fIstring\fR\fR] [\fB\-pair\ \fR\fB\fIarray\fR\fR] [\fB\-identity\ \fR\fB\fIinteger\fR\fR] [\fB\-box\ \fR\fB\fIboolean\fR\fR] [\fB\-boxcol\ \fR\fB\fIboolean\fR\fR] [\fB\-boxuse\ \fR\fB\fIstring\fR\fR] [\fB\-name\ \fR\fB\fIboolean\fR\fR] [\fB\-maxnamelen\ \fR\fB\fIinteger\fR\fR] [\fB\-number\ \fR\fB\fIboolean\fR\fR] [\fB\-listoptions\ \fR\fB\fIboolean\fR\fR] [\fB\-plurality\ \fR\fB\fIfloat\fR\fR] [\fB\-consensus\ \fR\fB\fIboolean\fR\fR] [\fB\-collision\ \fR\fB\fIboolean\fR\fR] [\fB\-alternative\ \fR\fB\fIlist\fR\fR] [\fB\-showscore\ \fR\fB\fIinteger\fR\fR] [\fB\-portrait\ \fR\fB\fIboolean\fR\fR] \fB\-graph\ \fR\fB\fIgraph\fR\fR .HP \w'\fBprettyplot\fR\ 'u \fBprettyplot\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBprettyplot\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Multiple,Display" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequences\fR \fIseqset\fR .RS 4 .RE .PP \fB\-matrixfile\fR \fImatrix\fR .RS 4 This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&. .RE .SS "Additional section" .PP \fB\-residuesperline\fR \fIinteger\fR .RS 4 The number of residues to be displayed on each line Default value: 50 .RE .PP \fB\-resbreak\fR \fIinteger\fR .RS 4 Default value: $(residuesperline) .RE .PP \fB\-ccolours\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-cidentity\fR \fIstring\fR .RS 4 Default value: RED .RE .PP \fB\-csimilarity\fR \fIstring\fR .RS 4 Default value: GREEN .RE .PP \fB\-cother\fR \fIstring\fR .RS 4 Default value: BLACK .RE .PP \fB\-docolour\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-shade\fR \fIstring\fR .RS 4 Set to BPLW for normal shading (black, pale, light, white) so for pair = 1\&.5,1\&.0,0\&.5 and shade = BPLW Residues score Colour 1\&.5 or over\&.\&.\&. BLACK (B) 1\&.0 to 1\&.5 \&.\&.\&. BROWN (P) 0\&.5 to 1\&.0 \&.\&.\&. WHEAT (L) under 0\&.5 \&.\&.\&.\&. WHITE (W) The only four letters allowed are BPLW, in any order\&. .RE .PP \fB\-pair\fR \fIarray\fR .RS 4 Default value: 1\&.5,1\&.0,0\&.5 .RE .PP \fB\-identity\fR \fIinteger\fR .RS 4 .RE .PP \fB\-box\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-boxcol\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-boxuse\fR \fIstring\fR .RS 4 Default value: GREY .RE .PP \fB\-name\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-maxnamelen\fR \fIinteger\fR .RS 4 Default value: 10 .RE .PP \fB\-number\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-listoptions\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-plurality\fR \fIfloat\fR .RS 4 Default value: @( $(sequences\&.totweight) / 2) .RE .SS "Consensus section" .PP \fB\-consensus\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-collision\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-alternative\fR \fIlist\fR .RS 4 Values are 0:Normal collision check\&. (default) 1:Compares identical scores with the max score found\&. So if any other residue matches the identical score then a collision has occurred\&. 2:If another residue has a greater than or equal to matching score and these do not match then a collision has occurred\&. 3:Checks all those not in the current consensus\&.If any of these give a top score for matching or identical scores then a collision has occured\&. .RE .PP \fB\-showscore\fR \fIinteger\fR .RS 4 Default value: \-1 .RE .PP \fB\-portrait\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Output section" .PP \fB\-graph\fR \fIgraph\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP prettyplot is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/biosed.1e0000644000000000000000000000553212214054043012455 0ustar '\" t .\" Title: BIOSED .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "BIOSED" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" biosed \- Replace or delete sequence sections .SH "SYNOPSIS" .HP \w'\fBbiosed\fR\ 'u \fBbiosed\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-targetregion\ \fR\fB\fIstring\fR\fR \fB\-delete\ \fR\fB\fItoggle\fR\fR \fB\-replace\ \fR\fB\fIstring\fR\fR [\fB\-position\ \fR\fB\fIinteger\fR\fR] \fB\-outseq\ \fR\fB\fIseqout\fR\fR .HP \w'\fBbiosed\fR\ 'u \fBbiosed\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBbiosed\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Required section" .PP \fB\-targetregion\fR \fIstring\fR .RS 4 Default value: N .RE .PP \fB\-delete\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-replace\fR \fIstring\fR .RS 4 Default value: A .RE .SS "Additional section" .PP \fB\-position\fR \fIinteger\fR .RS 4 .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqout\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP biosed is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/epestfind.1e0000644000000000000000000001052612214054043013170 0ustar '\" t .\" Title: EPESTFIND .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "EPESTFIND" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" epestfind \- Finds PEST motifs as potential proteolytic cleavage sites .SH "SYNOPSIS" .HP \w'\fBepestfind\fR\ 'u \fBepestfind\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-mwdata\ \fR\fB\fIdatafile\fR\fR] \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-order\ \fR\fB\fIselection\fR\fR [\fB\-threshold\ \fR\fB\fIfloat\fR\fR] \fB\-mono\ \fR\fB\fIboolean\fR\fR \fB\-potential\ \fR\fB\fIboolean\fR\fR \fB\-poor\ \fR\fB\fIboolean\fR\fR \fB\-invalid\ \fR\fB\fIboolean\fR\fR \fB\-map\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR .HP \w'\fBepestfind\fR\ 'u \fBepestfind\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBepestfind\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Motifs" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 Protein sequence USA to be analysed\&. .RE .PP \fB\-mwdata\fR \fIdatafile\fR .RS 4 Default value: Emolwt\&.dat .RE .SS "Required section" .PP \fB\-window\fR \fIinteger\fR .RS 4 Minimal distance between positively charged amino acids\&. Default value: 10 .RE .PP \fB\-order\fR \fIselection\fR .RS 4 Name of the output file which holds the results of the analysis\&. Results may be sorted by length, position and score\&. Default value: score .RE .SS "Additional section" .PP \fB\-threshold\fR \fIfloat\fR .RS 4 Threshold value to discriminate weak from potential PEST motifs\&. Valid PEST motifs are discriminated into \*(Aqpoor\*(Aq and \*(Aqpotential\*(Aq motifs depending on this threshold score\&. By default, the default value is set to +5\&.0 based on experimental data\&. Alterations are not recommended since significance is a matter of biology, not mathematics\&. Default value: +5\&.0 .RE .SS "Advanced section" .PP \fB\-mono\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-potential\fR \fIboolean\fR .RS 4 Decide whether potential PEST motifs should be printed\&. Default value: Y .RE .PP \fB\-poor\fR \fIboolean\fR .RS 4 Decide whether poor PEST motifs should be printed\&. Default value: Y .RE .PP \fB\-invalid\fR \fIboolean\fR .RS 4 Decide whether invalid PEST motifs should be printed\&. Default value: N .RE .PP \fB\-map\fR \fIboolean\fR .RS 4 Decide whether PEST motifs should be mapped to sequence\&. Default value: Y .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Name of file to which results will be written\&. .RE .PP \fB\-graph\fR \fIxygraph\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP epestfind is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/inforesidue.1e0000644000000000000000000000567512214054043013534 0ustar '\" t .\" Title: INFORESIDUE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "INFORESIDUE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" inforesidue \- Return information on a given amino acid residue .SH "SYNOPSIS" .HP \w'\fBinforesidue\fR\ 'u \fBinforesidue\fR \fB\-code\ \fR\fB\fIstring\fR\fR \fB\-aadata\ \fR\fB\fIdatafile\fR\fR \fB\-mwdata\ \fR\fB\fIdatafile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBinforesidue\fR\ 'u \fBinforesidue\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBinforesidue\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval:Chemistry data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-code\fR \fIstring\fR .RS 4 Enter IUPAC amino acids codes, e\&.g\&. A, C, D, E etc\&. Default value: ABCDEFGHIJKLMNOPQRSTUVWXYZ .RE .PP \fB\-aadata\fR \fIdatafile\fR .RS 4 Amino acid properties Default value: Eamino\&.dat .RE .PP \fB\-mwdata\fR \fIdatafile\fR .RS 4 Molecular weight data for amino acids Default value: Emolwt\&.dat .RE .SS "Required section" .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP inforesidue is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/tfextract.1e0000644000000000000000000000462212214054043013213 0ustar '\" t .\" Title: TFEXTRACT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "TFEXTRACT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" tfextract \- Process TRANSFAC transcription factor database for use by tfscan .SH "SYNOPSIS" .HP \w'\fBtfextract\fR\ 'u \fBtfextract\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR .HP \w'\fBtfextract\fR\ 'u \fBtfextract\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBtfextract\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP tfextract is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/prettyseq.1e0000644000000000000000000000621512214054043013247 0ustar '\" t .\" Title: PRETTYSEQ .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PRETTYSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" prettyseq \- Write a nucleotide sequence and its translation to file .SH "SYNOPSIS" .HP \w'\fBprettyseq\fR\ 'u \fBprettyseq\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-range\ \fR\fB\fIrange\fR\fR [\fB\-table\ \fR\fB\fIlist\fR\fR] [\fB\-ruler\ \fR\fB\fIboolean\fR\fR] [\fB\-plabel\ \fR\fB\fIboolean\fR\fR] [\fB\-nlabel\ \fR\fB\fIboolean\fR\fR] \fB\-width\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBprettyseq\fR\ 'u \fBprettyseq\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBprettyseq\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Translation,Display" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .SS "Required section" .PP \fB\-range\fR \fIrange\fR .RS 4 Default value: $(sequence\&.begin)\-$(sequence\&.end) .RE .SS "Additional section" .PP \fB\-table\fR \fIlist\fR .RS 4 .RE .PP \fB\-ruler\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-plabel\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-nlabel\fR \fIboolean\fR .RS 4 Default value: Y .RE .SS "Advanced section" .PP \fB\-width\fR \fIinteger\fR .RS 4 Default value: 60 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP prettyseq is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/urlget.1e0000644000000000000000000000473112214054043012512 0ustar '\" t .\" Title: URLGET .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "URLGET" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" urlget \- Get URLs of data resources .SH "SYNOPSIS" .HP \w'\fBurlget\fR\ 'u \fBurlget\fR \fB\-url\ \fR\fB\fIurl\fR\fR \fB\-outfile\ \fR\fB\fIouturl\fR\fR .HP \w'\fBurlget\fR\ 'u \fBurlget\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBurlget\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval:Url data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-url\fR \fIurl\fR .RS 4 .RE .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIouturl\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP urlget is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/dbfetchtest.1e0000644000000000000000000000524512214054043013510 0ustar '\" t .\" Title: DBFETCHTEST .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DBFETCHTEST" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" dbfetchtest \- Generates server cache file for WSDbfetch data sources .SH "SYNOPSIS" .HP \w'\fBdbfetchtest\fR\ 'u \fBdbfetchtest\fR \fB\-servername\ \fR\fB\fIstring\fR\fR [\fB\-runtestqueries\ \fR\fB\fIboolean\fR\fR] [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] .HP \w'\fBdbfetchtest\fR\ 'u \fBdbfetchtest\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdbfetchtest\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Display,Information" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-servername\fR \fIstring\fR .RS 4 Default value: dbfetch .RE .PP \fB\-runtestqueries\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP dbfetchtest is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fuzztran.1e0000644000000000000000000000760612214054043013077 0ustar '\" t .\" Title: FUZZTRAN .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "FUZZTRAN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fuzztran \- Search for patterns in protein sequences (translated) .SH "SYNOPSIS" .HP \w'\fBfuzztran\fR\ 'u \fBfuzztran\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-pattern\ \fR\fB\fIpattern\fR\fR [\fB\-frame\ \fR\fB\fIlist\fR\fR] [\fB\-table\ \fR\fB\fIlist\fR\fR] \fB\-outfile\ \fR\fB\fIreport\fR\fR .HP \w'\fBfuzztran\fR\ 'u \fBfuzztran\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfuzztran\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Motifs,Protein:Motifs" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-pattern\fR \fIpattern\fR .RS 4 The standard IUPAC one\-letter codes for the amino acids are used\&. The symbol \*(Aqx\*(Aq is used for a position where any amino acid is accepted\&. Ambiguities are indicated by listing the acceptable amino acids for a given position, between square parentheses \*(Aq[ ]\*(Aq\&. For example: [ALT] stands for Ala or Leu or Thr\&. Ambiguities are also indicated by listing between a pair of curly brackets \*(Aq{ }\*(Aq the amino acids that are not accepted at a gven position\&. For example: {AM} stands for any amino acid except Ala and Met\&. Each element in a pattern is separated from its neighbor by a \*(Aq\-\*(Aq\&. (Optional in fuzztran) Repetition of an element of the pattern can be indicated by following that element with a numerical value or a numerical range between parenthesis\&. Examples: x(3) corresponds to x\-x\-x, x(2,4) corresponds to x\-x or x\-x\-x or x\-x\-x\-x\&. When a pattern is restricted to either the N\- or C\-terminal of a sequence, that pattern either starts with a \*(Aq<\*(Aq symbol or respectively ends with a \*(Aq>\*(Aq symbol\&. A period ends the pattern\&. (Optional in fuzztran)\&. For example, [DE](2)HS{P}X(2)PX(2,4)C .RE .SS "Additional section" .PP \fB\-frame\fR \fIlist\fR .RS 4 Default value: 1 .RE .PP \fB\-table\fR \fIlist\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIreport\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fuzztran is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/btwisted.1e0000644000000000000000000000536012214054043013034 0ustar '\" t .\" Title: BTWISTED .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "BTWISTED" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" btwisted \- Calculate the twisting in a B\-DNA sequence .SH "SYNOPSIS" .HP \w'\fBbtwisted\fR\ 'u \fBbtwisted\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-angledata\ \fR\fB\fIdatafile\fR\fR \fB\-energydata\ \fR\fB\fIdatafile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBbtwisted\fR\ 'u \fBbtwisted\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBbtwisted\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Properties,Nucleic:Composition,Nucleic:2D structure" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .PP \fB\-angledata\fR \fIdatafile\fR .RS 4 Default value: Eangles\&.dat .RE .PP \fB\-energydata\fR \fIdatafile\fR .RS 4 Default value: Eenergy\&.dat .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP btwisted is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/distmat.1e0000644000000000000000000000777112214054043012664 0ustar '\" t .\" Title: DISTMAT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DISTMAT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" distmat \- Create a distance matrix from a multiple sequence alignment .SH "SYNOPSIS" .HP \w'\fBdistmat\fR\ 'u \fBdistmat\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR \fB\-nucmethod\ \fR\fB\fIlist\fR\fR \fB\-protmethod\ \fR\fB\fIlist\fR\fR \fB\-ambiguous\ \fR\fB\fIboolean\fR\fR \fB\-gapweight\ \fR\fB\fIfloat\fR\fR \fB\-position\ \fR\fB\fIinteger\fR\fR \fB\-calculatea\ \fR\fB\fIboolean\fR\fR \fB\-parametera\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBdistmat\fR\ 'u \fBdistmat\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdistmat\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Phylogeny:Molecular sequence" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqset\fR .RS 4 File containing a sequence alignment\&. .RE .SS "Required section" .PP \fB\-nucmethod\fR \fIlist\fR .RS 4 Multiple substitution correction methods for nucleotides\&. .RE .PP \fB\-protmethod\fR \fIlist\fR .RS 4 Multiple substitution correction methods for proteins\&. .RE .SS "Additional section" .PP \fB\-ambiguous\fR \fIboolean\fR .RS 4 Option to use the ambiguous codes in the calculation of the Jukes\-Cantor method or if the sequences are proteins\&. Default value: N .RE .PP \fB\-gapweight\fR \fIfloat\fR .RS 4 Option to weight gaps in the uncorrected (nucleotide) and Jukes\-Cantor distance methods\&. Default value: 0\&. .RE .PP \fB\-position\fR \fIinteger\fR .RS 4 Choose base positions to analyse in each codon i\&.e\&. 123 (all bases), 12 (the first two bases), 1, 2, or 3 individual bases\&. Default value: 123 .RE .PP \fB\-calculatea\fR \fIboolean\fR .RS 4 This will force the calculation of parameter \*(Aqa\*(Aq in the Jin\-Nei Gamma distance calculation, otherwise the default is 1\&.0 (see \-parametera option)\&. Default value: N .RE .PP \fB\-parametera\fR \fIfloat\fR .RS 4 User defined parameter \*(Aqa\*(Aq to be use in the Jin\-Nei Gamma distance calculation\&. The suggested value to be used is 1\&.0 (Jin et al\&.) and this is the default\&. Default value: 1\&.0 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP distmat is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/plotorf.1e0000644000000000000000000000532712214054043012677 0ustar '\" t .\" Title: PLOTORF .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PLOTORF" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" plotorf \- Plot potential open reading frames in a nucleotide sequence .SH "SYNOPSIS" .HP \w'\fBplotorf\fR\ 'u \fBplotorf\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-start\ \fR\fB\fIstring\fR\fR \fB\-stop\ \fR\fB\fIstring\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR .HP \w'\fBplotorf\fR\ 'u \fBplotorf\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBplotorf\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Gene finding,Nucleic:Translation,Display" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .SS "Advanced section" .PP \fB\-start\fR \fIstring\fR .RS 4 Default value: ATG .RE .PP \fB\-stop\fR \fIstring\fR .RS 4 Default value: TAA,TAG,TGA .RE .SS "Output section" .PP \fB\-graph\fR \fIxygraph\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP plotorf is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/helixturnhelix.1e0000644000000000000000000000570012214054043014261 0ustar '\" t .\" Title: HELIXTURNHELIX .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "HELIXTURNHELIX" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" helixturnhelix \- Identify nucleic acid\-binding motifs in protein sequences .SH "SYNOPSIS" .HP \w'\fBhelixturnhelix\fR\ 'u \fBhelixturnhelix\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-mean\ \fR\fB\fIfloat\fR\fR] [\fB\-sd\ \fR\fB\fIfloat\fR\fR] [\fB\-minsd\ \fR\fB\fIfloat\fR\fR] [\fB\-eightyseven\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIreport\fR\fR .HP \w'\fBhelixturnhelix\fR\ 'u \fBhelixturnhelix\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBhelixturnhelix\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:2D Structure,Protein:Domains" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Additional section" .PP \fB\-mean\fR \fIfloat\fR .RS 4 Default value: 238\&.71 .RE .PP \fB\-sd\fR \fIfloat\fR .RS 4 Default value: 293\&.61 .RE .PP \fB\-minsd\fR \fIfloat\fR .RS 4 Default value: 2\&.5 .RE .PP \fB\-eightyseven\fR \fIboolean\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIreport\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP helixturnhelix is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/listor.1e0000644000000000000000000000611112214054043012516 0ustar '\" t .\" Title: LISTOR .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "LISTOR" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" listor \- Write a list file of the logical OR of two sets of sequences .SH "SYNOPSIS" .HP \w'\fBlistor\fR\ 'u \fBlistor\fR \fB\-firstsequences\ \fR\fB\fIseqset\fR\fR \fB\-secondsequences\ \fR\fB\fIseqset\fR\fR [\fB\-operator\ \fR\fB\fIlist\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBlistor\fR\ 'u \fBlistor\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBlistor\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-firstsequences\fR \fIseqset\fR .RS 4 .RE .PP \fB\-secondsequences\fR \fIseqset\fR .RS 4 .RE .SS "Additional section" .PP \fB\-operator\fR \fIlist\fR .RS 4 The following logical operators combine the sequences in the following ways: OR \- gives all that occur in one set or the other AND \- gives only those which occur in both sets XOR \- gives those which only occur in one set or the other, but not in both NOT \- gives those which occur in the first set except for those that also occur in the second Default value: OR .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 The list of sequence names will be written to this list file .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP listor is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/jaspextract.1e0000644000000000000000000000473512214054043013544 0ustar '\" t .\" Title: JASPEXTRACT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "JASPEXTRACT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" jaspextract \- Extract data from JASPAR .SH "SYNOPSIS" .HP \w'\fBjaspextract\fR\ 'u \fBjaspextract\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR .HP \w'\fBjaspextract\fR\ 'u \fBjaspextract\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBjaspextract\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-directory\fR \fIdirectory\fR .RS 4 The FlatFileDir directory containing the \&.pfm files and the matrix_list\&.txt file .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP jaspextract is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/dan.1e0000644000000000000000000001250512214054043011750 0ustar '\" t .\" Title: DAN .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DAN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" dan \- Calculates nucleic acid melting temperature .SH "SYNOPSIS" .HP \w'\fBdan\fR\ 'u \fBdan\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-windowsize\ \fR\fB\fIinteger\fR\fR \fB\-shiftincrement\ \fR\fB\fIinteger\fR\fR \fB\-dnaconc\ \fR\fB\fIfloat\fR\fR \fB\-saltconc\ \fR\fB\fIfloat\fR\fR [\fB\-product\ \fR\fB\fItoggle\fR\fR] \fB\-formamide\ \fR\fB\fIfloat\fR\fR \fB\-mismatch\ \fR\fB\fIfloat\fR\fR \fB\-prodlen\ \fR\fB\fIinteger\fR\fR [\fB\-thermo\ \fR\fB\fItoggle\fR\fR] \fB\-temperature\ \fR\fB\fIfloat\fR\fR \fB\-rna\ \fR\fB\fIboolean\fR\fR \fB\-plot\ \fR\fB\fItoggle\fR\fR \fB\-mintemp\ \fR\fB\fIfloat\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR .HP \w'\fBdan\fR\ 'u \fBdan\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdan\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Properties,Nucleic:Composition" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Required section" .PP \fB\-windowsize\fR \fIinteger\fR .RS 4 The values of melting point and other thermodynamic properties of the sequence are determined by taking a short length of sequence known as a window and determining the properties of the sequence in that window\&. The window is incrementally moved along the sequence with the properties being calculated at each new position\&. Default value: 20 .RE .PP \fB\-shiftincrement\fR \fIinteger\fR .RS 4 This is the amount by which the window is moved at each increment in order to find the melting point and other properties along the sequence\&. Default value: 1 .RE .PP \fB\-dnaconc\fR \fIfloat\fR .RS 4 Default value: 50\&. .RE .PP \fB\-saltconc\fR \fIfloat\fR .RS 4 Default value: 50\&. .RE .SS "Additional section" .SS "Product options" .PP \fB\-product\fR \fItoggle\fR .RS 4 This prompts for percent formamide, percent of mismatches allowed and product length\&. .RE .PP \fB\-formamide\fR \fIfloat\fR .RS 4 This specifies the percent formamide to be used in calculations (it is ignored unless \-product is used)\&. Default value: 0\&. .RE .PP \fB\-mismatch\fR \fIfloat\fR .RS 4 This specifies the percent mismatch to be used in calculations (it is ignored unless \-product is used)\&. Default value: 0\&. .RE .PP \fB\-prodlen\fR \fIinteger\fR .RS 4 This specifies the product length to be used in calculations (it is ignored unless \-product is used)\&. Default value: $(windowsize) .RE .SS "Thermodynamic options" .PP \fB\-thermo\fR \fItoggle\fR .RS 4 Output the DeltaG, DeltaH and DeltaS values of the sequence windows to the output data file\&. .RE .PP \fB\-temperature\fR \fIfloat\fR .RS 4 If \-thermo has been specified then this specifies the temperature at which to calculate the DeltaG, DeltaH and DeltaS values\&. Default value: 25\&. .RE .SS "Advanced section" .PP \fB\-rna\fR \fIboolean\fR .RS 4 This specifies that the sequence is an RNA sequence and not a DNA sequence\&. .RE .SS "Output section" .PP \fB\-plot\fR \fItoggle\fR .RS 4 If this is not specified then the file of output data is produced, else a plot of the melting point along the sequence is produced\&. .RE .PP \fB\-mintemp\fR \fIfloat\fR .RS 4 Enter a minimum value for the temperature scale (y\-axis) of the plot\&. Default value: 55\&. .RE .PP \fB\-graph\fR \fIxygraph\fR .RS 4 .RE .PP \fB\-outfile\fR \fIreport\fR .RS 4 If a plot is not being produced then data on the melting point etc\&. in each window along the sequence is output to the file\&. .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP dan is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/dbxobo.1e0000644000000000000000000000675512214054043012475 0ustar '\" t .\" Title: DBXOBO .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DBXOBO" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" dbxobo \- Index an obo ontology using b+tree indices .SH "SYNOPSIS" .HP \w'\fBdbxobo\fR\ 'u \fBdbxobo\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-standardname\ \fR\fB\fIstring\fR\fR \fB\-dbresource\ \fR\fB\fIstring\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-filenames\ \fR\fB\fIstring\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-compressed\ \fR\fB\fIboolean\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBdbxobo\fR\ 'u \fBdbxobo\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdbxobo\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-dbname\fR \fIstring\fR .RS 4 .RE .PP \fB\-standardname\fR \fIstring\fR .RS 4 Default value: $(dbname) .RE .PP \fB\-dbresource\fR \fIstring\fR .RS 4 Default value: oboresource .RE .PP \fB\-directory\fR \fIdirectory\fR .RS 4 Default value: \&. .RE .PP \fB\-filenames\fR \fIstring\fR .RS 4 Default value: *\&.obo .RE .SS "Required section" .PP \fB\-fields\fR \fIlist\fR .RS 4 Default value: * .RE .PP \fB\-compressed\fR \fIboolean\fR .RS 4 Default value: Y .RE .SS "Advanced section" .PP \fB\-release\fR \fIstring\fR .RS 4 Default value: 0\&.0 .RE .PP \fB\-date\fR \fIstring\fR .RS 4 Default value: 00/00/00 .RE .PP \fB\-exclude\fR \fIstring\fR .RS 4 .RE .SS "Output section" .PP \fB\-indexoutdir\fR \fIoutdir\fR .RS 4 Default value: \&. .RE .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP dbxobo is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/edamdef.1e0000644000000000000000000000616412214054043012577 0ustar '\" t .\" Title: EDAMDEF .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "EDAMDEF" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" edamdef \- Find EDAM ontology terms by definition .SH "SYNOPSIS" .HP \w'\fBedamdef\fR\ 'u \fBedamdef\fR \fB\-query\ \fR\fB\fIstring\fR\fR [\fB\-namespace\ \fR\fB\fIlist\fR\fR] \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-edamdef\ \fR\fB\fIoutobo\fR\fR .HP \w'\fBedamdef\fR\ 'u \fBedamdef\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBedamdef\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Data retrieval:Ontology data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-query\fR \fIstring\fR .RS 4 .RE .SS "Additional section" .PP \fB\-namespace\fR \fIlist\fR .RS 4 By default all terms are returned\&. Searches can be limited to one or a few namespaces\&. Default value: * .RE .SS "Advanced section" .PP \fB\-subclasses\fR \fIboolean\fR .RS 4 Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: N .RE .PP \fB\-obsolete\fR \fIboolean\fR .RS 4 The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N .RE .SS "Output section" .PP \fB\-edamdef\fR \fIoutobo\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP edamdef is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/garnier.1e0000644000000000000000000000611012214054043012630 0ustar '\" t .\" Title: GARNIER .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "GARNIER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" garnier \- Predicts protein secondary structure using GOR method .SH "SYNOPSIS" .HP \w'\fBgarnier\fR\ 'u \fBgarnier\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-idc\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR .HP \w'\fBgarnier\fR\ 'u \fBgarnier\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBgarnier\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:2D Structure" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Advanced section" .PP \fB\-idc\fR \fIinteger\fR .RS 4 In their paper, GOR mention that if you know something about the secondary structure content of the protein you are analyzing, you can do better in prediction\&. \*(Aqidc\*(Aq is an index into a set of arrays, dharr[] and dsarr[], which provide \*(Aqdecision constants\*(Aq (dch, dcs), which are offsets that are applied to the weights for the helix and sheet (extend) terms\&. So, idc=0 says don\*(Aqt use the decision constant offsets, and idc=1 to 6 indicates that various combinations of dch,dcs offsets should be used\&. .RE .SS "Output section" .PP \fB\-outfile\fR \fIreport\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP garnier is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/newcpgreport.1e0000644000000000000000000000576612214054043013740 0ustar '\" t .\" Title: NEWCPGREPORT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "NEWCPGREPORT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" newcpgreport \- Identify CpG islands in nucleotide sequence(s) .SH "SYNOPSIS" .HP \w'\fBnewcpgreport\fR\ 'u \fBnewcpgreport\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-shift\ \fR\fB\fIinteger\fR\fR \fB\-minlen\ \fR\fB\fIinteger\fR\fR \fB\-minoe\ \fR\fB\fIfloat\fR\fR \fB\-minpc\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBnewcpgreport\fR\ 'u \fBnewcpgreport\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBnewcpgreport\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:CpG Islands" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Required section" .PP \fB\-window\fR \fIinteger\fR .RS 4 Default value: 100 .RE .PP \fB\-shift\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-minlen\fR \fIinteger\fR .RS 4 Default value: 200 .RE .PP \fB\-minoe\fR \fIfloat\fR .RS 4 Default value: 0\&.6 .RE .PP \fB\-minpc\fR \fIfloat\fR .RS 4 Default value: 50\&. .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP newcpgreport is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/dbifasta.1e0000644000000000000000000000745612214054043012774 0ustar '\" t .\" Title: DBIFASTA .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DBIFASTA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" dbifasta \- Index a fasta file database .SH "SYNOPSIS" .HP \w'\fBdbifasta\fR\ 'u \fBdbifasta\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-idformat\ \fR\fB\fIlist\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-filenames\ \fR\fB\fIstring\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-maxindex\ \fR\fB\fIinteger\fR\fR \fB\-sortoptions\ \fR\fB\fIstring\fR\fR \fB\-systemsort\ \fR\fB\fIboolean\fR\fR \fB\-cleanup\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR .HP \w'\fBdbifasta\fR\ 'u \fBdbifasta\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdbifasta\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-dbname\fR \fIstring\fR .RS 4 .RE .PP \fB\-idformat\fR \fIlist\fR .RS 4 Default value: idacc .RE .PP \fB\-directory\fR \fIdirectory\fR .RS 4 Default value: \&. .RE .PP \fB\-filenames\fR \fIstring\fR .RS 4 Default value: *\&.dat .RE .SS "Required section" .PP \fB\-release\fR \fIstring\fR .RS 4 Default value: 0\&.0 .RE .PP \fB\-date\fR \fIstring\fR .RS 4 Default value: 00/00/00 .RE .SS "Advanced section" .PP \fB\-fields\fR \fIlist\fR .RS 4 Default value: acc .RE .PP \fB\-exclude\fR \fIstring\fR .RS 4 .RE .PP \fB\-maxindex\fR \fIinteger\fR .RS 4 .RE .PP \fB\-sortoptions\fR \fIstring\fR .RS 4 Sort options, typically \*(Aq\-T \&.\*(Aq to use current directory for work files and \*(Aq\-k 1,1\*(Aq to force GNU sort to use the first field Default value: \-T \&. \-k 1,1 .RE .PP \fB\-systemsort\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-cleanup\fR \fIboolean\fR .RS 4 Default value: Y .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-indexoutdir\fR \fIoutdir\fR .RS 4 Default value: \&. .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP dbifasta is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/nthseq.1e0000644000000000000000000000510212214054043012503 0ustar '\" t .\" Title: NTHSEQ .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "NTHSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" nthseq \- Write to file a single sequence from an input stream of sequences .SH "SYNOPSIS" .HP \w'\fBnthseq\fR\ 'u \fBnthseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-number\ \fR\fB\fIinteger\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR .HP \w'\fBnthseq\fR\ 'u \fBnthseq\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBnthseq\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Required section" .PP \fB\-number\fR \fIinteger\fR .RS 4 Default value: 1 .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqout\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP nthseq is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/dbxtax.1e0000644000000000000000000000632512214054043012503 0ustar '\" t .\" Title: DBXTAX .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DBXTAX" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" dbxtax \- Index NCBI taxonomy using b+tree indices .SH "SYNOPSIS" .HP \w'\fBdbxtax\fR\ 'u \fBdbxtax\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-dbresource\ \fR\fB\fIstring\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-compressed\ \fR\fB\fIboolean\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBdbxtax\fR\ 'u \fBdbxtax\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdbxtax\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-dbname\fR \fIstring\fR .RS 4 Default value: taxon .RE .PP \fB\-dbresource\fR \fIstring\fR .RS 4 Default value: taxresource .RE .PP \fB\-directory\fR \fIdirectory\fR .RS 4 Default value: \&. .RE .SS "Required section" .PP \fB\-fields\fR \fIlist\fR .RS 4 Default value: * .RE .PP \fB\-compressed\fR \fIboolean\fR .RS 4 Default value: Y .RE .SS "Advanced section" .PP \fB\-release\fR \fIstring\fR .RS 4 Default value: 0\&.0 .RE .PP \fB\-date\fR \fIstring\fR .RS 4 Default value: 00/00/00 .RE .SS "Output section" .PP \fB\-indexoutdir\fR \fIoutdir\fR .RS 4 Default value: \&. .RE .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP dbxtax is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/primersearch.1e0000644000000000000000000000530212214054043013667 0ustar '\" t .\" Title: PRIMERSEARCH .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PRIMERSEARCH" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" primersearch \- Search DNA sequences for matches with primer pairs .SH "SYNOPSIS" .HP \w'\fBprimersearch\fR\ 'u \fBprimersearch\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-mismatchpercent\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBprimersearch\fR\ 'u \fBprimersearch\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBprimersearch\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Primers" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-seqall\fR \fIseqall\fR .RS 4 .RE .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .SS "Required section" .PP \fB\-mismatchpercent\fR \fIinteger\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP primersearch is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/dbxedam.1e0000644000000000000000000000702112214054043012607 0ustar '\" t .\" Title: DBXEDAM .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DBXEDAM" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" dbxedam \- Index the EDAM ontology using b+tree indices .SH "SYNOPSIS" .HP \w'\fBdbxedam\fR\ 'u \fBdbxedam\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-standardname\ \fR\fB\fIstring\fR\fR \fB\-dbresource\ \fR\fB\fIstring\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-filenames\ \fR\fB\fIstring\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-compressed\ \fR\fB\fIboolean\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBdbxedam\fR\ 'u \fBdbxedam\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdbxedam\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-dbname\fR \fIstring\fR .RS 4 Default value: edam .RE .PP \fB\-standardname\fR \fIstring\fR .RS 4 Default value: $(dbname) .RE .PP \fB\-dbresource\fR \fIstring\fR .RS 4 Default value: edamresource .RE .PP \fB\-directory\fR \fIdirectory\fR .RS 4 Default value: \&. .RE .PP \fB\-filenames\fR \fIstring\fR .RS 4 Default value: EDAM*\&.obo .RE .SS "Required section" .PP \fB\-fields\fR \fIlist\fR .RS 4 Default value: * .RE .PP \fB\-compressed\fR \fIboolean\fR .RS 4 Default value: Y .RE .SS "Advanced section" .PP \fB\-release\fR \fIstring\fR .RS 4 Default value: 0\&.0 .RE .PP \fB\-date\fR \fIstring\fR .RS 4 Default value: 00/00/00 .RE .PP \fB\-exclude\fR \fIstring\fR .RS 4 .RE .SS "Output section" .PP \fB\-indexoutdir\fR \fIoutdir\fR .RS 4 Default value: \&. .RE .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP dbxedam is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/newseq.1e0000644000000000000000000000631412214054043012511 0ustar '\" t .\" Title: NEWSEQ .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "NEWSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" newseq \- Create a sequence file from a typed\-in sequence .SH "SYNOPSIS" .HP \w'\fBnewseq\fR\ 'u \fBnewseq\fR \fB\-name\ \fR\fB\fIstring\fR\fR \fB\-description\ \fR\fB\fIstring\fR\fR \fB\-type\ \fR\fB\fIlist\fR\fR \fB\-sequence\ \fR\fB\fIstring\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR .HP \w'\fBnewseq\fR\ 'u \fBnewseq\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBnewseq\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-name\fR \fIstring\fR .RS 4 The name of of the sequence should be a single word that you will use to identify the sequence\&. It should have no (or few) punctuation characters in it\&. .RE .PP \fB\-description\fR \fIstring\fR .RS 4 Enter any description of the sequence that you require\&. .RE .PP \fB\-type\fR \fIlist\fR .RS 4 Default value: N .RE .PP \fB\-sequence\fR \fIstring\fR .RS 4 The sequence itself\&. Because of the limitation of the operating system, you will only be able to type in a short sequence of (typically) 250 characters, or so\&. The keyboard will beep at you when you have reached this limit and you will not be able to press the RETURN/ENTER key until you have deleted a few characters\&. .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqout\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP newseq is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/dbxfasta.1e0000644000000000000000000000674112214054043013007 0ustar '\" t .\" Title: DBXFASTA .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DBXFASTA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" dbxfasta \- Index a fasta file database using b+tree indices .SH "SYNOPSIS" .HP \w'\fBdbxfasta\fR\ 'u \fBdbxfasta\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-dbresource\ \fR\fB\fIstring\fR\fR \fB\-idformat\ \fR\fB\fIlist\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-filenames\ \fR\fB\fIstring\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-compressed\ \fR\fB\fIboolean\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBdbxfasta\fR\ 'u \fBdbxfasta\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdbxfasta\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-dbname\fR \fIstring\fR .RS 4 .RE .PP \fB\-dbresource\fR \fIstring\fR .RS 4 .RE .PP \fB\-idformat\fR \fIlist\fR .RS 4 Default value: idacc .RE .PP \fB\-directory\fR \fIdirectory\fR .RS 4 Default value: \&. .RE .PP \fB\-filenames\fR \fIstring\fR .RS 4 Default value: *\&.fasta .RE .SS "Required section" .PP \fB\-fields\fR \fIlist\fR .RS 4 Default value: id,acc .RE .PP \fB\-compressed\fR \fIboolean\fR .RS 4 Default value: Y .RE .SS "Advanced section" .PP \fB\-release\fR \fIstring\fR .RS 4 Default value: 0\&.0 .RE .PP \fB\-date\fR \fIstring\fR .RS 4 Default value: 00/00/00 .RE .PP \fB\-exclude\fR \fIstring\fR .RS 4 .RE .SS "Output section" .PP \fB\-indexoutdir\fR \fIoutdir\fR .RS 4 Default value: \&. .RE .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP dbxfasta is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/mwfilter.1e0000644000000000000000000000550712214054043013043 0ustar '\" t .\" Title: MWFILTER .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "MWFILTER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" mwfilter \- Filter noisy data from molecular weights file .SH "SYNOPSIS" .HP \w'\fBmwfilter\fR\ 'u \fBmwfilter\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-datafile\ \fR\fB\fIdatafile\fR\fR \fB\-tolerance\ \fR\fB\fIfloat\fR\fR [\fB\-showdel\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBmwfilter\fR\ 'u \fBmwfilter\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBmwfilter\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Composition" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .PP \fB\-datafile\fR \fIdatafile\fR .RS 4 Default value: Emwfilter\&.dat .RE .SS "Required section" .PP \fB\-tolerance\fR \fIfloat\fR .RS 4 Default value: 50\&.0 .RE .SS "Additional section" .PP \fB\-showdel\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP mwfilter is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/degapseq.1e0000644000000000000000000000474212214054043013003 0ustar '\" t .\" Title: DEGAPSEQ .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DEGAPSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" degapseq \- Removes non\-alphabetic (e\&.g\&. gap) characters from sequences .SH "SYNOPSIS" .HP \w'\fBdegapseq\fR\ 'u \fBdegapseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBdegapseq\fR\ 'u \fBdegapseq\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdegapseq\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP degapseq is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/seqretsetall.1e0000644000000000000000000000511612214054043013716 0ustar '\" t .\" Title: SEQRETSETALL .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SEQRETSETALL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" seqretsetall \- Reads and writes (returns) many sets of sequences .SH "SYNOPSIS" .HP \w'\fBseqretsetall\fR\ 'u \fBseqretsetall\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBseqretsetall\fR\ 'u \fBseqretsetall\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBseqretsetall\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-feature\fR \fIboolean\fR .RS 4 .RE .PP \fB\-sequence\fR \fIseqsetall\fR .RS 4 .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP seqretsetall is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/pepwheel.1e0000644000000000000000000000743712214054043013027 0ustar '\" t .\" Title: PEPWHEEL .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PEPWHEEL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" pepwheel \- Draw a helical wheel diagram for a protein sequence .SH "SYNOPSIS" .HP \w'\fBpepwheel\fR\ 'u \fBpepwheel\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-wheel\ \fR\fB\fIboolean\fR\fR [\fB\-steps\ \fR\fB\fIinteger\fR\fR] [\fB\-turns\ \fR\fB\fIinteger\fR\fR] \fB\-graph\ \fR\fB\fIgraph\fR\fR \fB\-amphipathic\ \fR\fB\fItoggle\fR\fR \fB\-squares\ \fR\fB\fIstring\fR\fR \fB\-diamonds\ \fR\fB\fIstring\fR\fR \fB\-octags\ \fR\fB\fIstring\fR\fR .HP \w'\fBpepwheel\fR\ 'u \fBpepwheel\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBpepwheel\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Display,Protein:2D Structure" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .SS "Output section" .PP \fB\-wheel\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-steps\fR \fIinteger\fR .RS 4 The number of residues plotted per turn is this value divided by the \*(Aqturns\*(Aq value\&. Default value: 18 .RE .PP \fB\-turns\fR \fIinteger\fR .RS 4 The number of residues plotted per turn is the \*(Aqsteps\*(Aq value divided by this value\&. Default value: 5 .RE .PP \fB\-graph\fR \fIgraph\fR .RS 4 .RE .SS "Markup section" .PP \fB\-amphipathic\fR \fItoggle\fR .RS 4 If this is true then the residues ACFGILMVWY are marked as squares and all other residues are unmarked\&. This overrides any other markup that you may have specified using the qualifiers \*(Aq\-squares\*(Aq, \*(Aq\-diamonds\*(Aq and \*(Aq\-octags\*(Aq\&. .RE .PP \fB\-squares\fR \fIstring\fR .RS 4 By default the aliphatic residues ILVM are marked with squares\&. Default value: ILVM .RE .PP \fB\-diamonds\fR \fIstring\fR .RS 4 By default the residues DENQST are marked with diamonds\&. Default value: DENQST .RE .PP \fB\-octags\fR \fIstring\fR .RS 4 By default the positively charged residues HKR are marked with octagons\&. Default value: HKR .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP pepwheel is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/hmoment.1e0000644000000000000000000000624512214054043012661 0ustar '\" t .\" Title: HMOMENT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "HMOMENT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" hmoment \- Calculate and plot hydrophobic moment for protein sequence(s) .SH "SYNOPSIS" .HP \w'\fBhmoment\fR\ 'u \fBhmoment\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR [\fB\-window\ \fR\fB\fIinteger\fR\fR] [\fB\-aangle\ \fR\fB\fIinteger\fR\fR] [\fB\-bangle\ \fR\fB\fIinteger\fR\fR] \fB\-baseline\ \fR\fB\fIfloat\fR\fR \fB\-plot\ \fR\fB\fItoggle\fR\fR \fB\-double\ \fR\fB\fIboolean\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBhmoment\fR\ 'u \fBhmoment\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBhmoment\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Properties" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-seqall\fR \fIseqall\fR .RS 4 .RE .SS "Additional section" .PP \fB\-window\fR \fIinteger\fR .RS 4 Default value: 10 .RE .PP \fB\-aangle\fR \fIinteger\fR .RS 4 Default value: 100 .RE .PP \fB\-bangle\fR \fIinteger\fR .RS 4 Default value: 160 .RE .SS "Advanced section" .PP \fB\-baseline\fR \fIfloat\fR .RS 4 Default value: 0\&.35 .RE .SS "Output section" .PP \fB\-plot\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-double\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-graph\fR \fIxygraph\fR .RS 4 .RE .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP hmoment is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/redata.1e0000644000000000000000000000616112214054043012447 0ustar '\" t .\" Title: REDATA .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "REDATA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" redata \- Retrieve information from REBASE restriction enzyme database .SH "SYNOPSIS" .HP \w'\fBredata\fR\ 'u \fBredata\fR \fB\-enzyme\ \fR\fB\fIstring\fR\fR \fB\-isoschizomers\ \fR\fB\fIboolean\fR\fR \fB\-references\ \fR\fB\fIboolean\fR\fR \fB\-suppliers\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBredata\fR\ 'u \fBredata\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBredata\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Restriction" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-enzyme\fR \fIstring\fR .RS 4 Enter the name of the restriction enzyme that you wish to get details of\&. The names often have a \*(AqI\*(Aq in them \- this is a capital \*(Aqi\*(Aq, not a \*(Aq1\*(Aq or an \*(Aql\*(Aq\&. The names are case\-independent (\*(AqAaeI\*(Aq is the same as \*(Aqaaei\*(Aq) Default value: BamHI .RE .SS "Output section" .PP \fB\-isoschizomers\fR \fIboolean\fR .RS 4 Show other enzymes with this specificity\&. (Isoschizomers) Default value: Y .RE .PP \fB\-references\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-suppliers\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP redata is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/twofeat.1e0000644000000000000000000003107612214054043012663 0ustar '\" t .\" Title: TWOFEAT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "TWOFEAT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" twofeat \- Finds neighbouring pairs of features in sequence(s) .SH "SYNOPSIS" .HP \w'\fBtwofeat\fR\ 'u \fBtwofeat\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-asource\ \fR\fB\fIstring\fR\fR] \fB\-atype\ \fR\fB\fIstring\fR\fR [\fB\-asense\ \fR\fB\fIlist\fR\fR] [\fB\-aminscore\ \fR\fB\fIfloat\fR\fR] [\fB\-amaxscore\ \fR\fB\fIfloat\fR\fR] [\fB\-atag\ \fR\fB\fIstring\fR\fR] [\fB\-avalue\ \fR\fB\fIstring\fR\fR] [\fB\-bsource\ \fR\fB\fIstring\fR\fR] \fB\-btype\ \fR\fB\fIstring\fR\fR [\fB\-bsense\ \fR\fB\fIlist\fR\fR] [\fB\-bminscore\ \fR\fB\fIfloat\fR\fR] [\fB\-bmaxscore\ \fR\fB\fIfloat\fR\fR] [\fB\-btag\ \fR\fB\fIstring\fR\fR] [\fB\-bvalue\ \fR\fB\fIstring\fR\fR] [\fB\-overlap\ \fR\fB\fIlist\fR\fR] \fB\-minrange\ \fR\fB\fIinteger\fR\fR \fB\-maxrange\ \fR\fB\fIinteger\fR\fR [\fB\-rangetype\ \fR\fB\fIlist\fR\fR] [\fB\-sense\ \fR\fB\fIlist\fR\fR] [\fB\-order\ \fR\fB\fIlist\fR\fR] [\fB\-twoout\ \fR\fB\fItoggle\fR\fR] \fB\-typeout\ \fR\fB\fIstring\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR .HP \w'\fBtwofeat\fR\ 'u \fBtwofeat\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBtwofeat\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Feature tables" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "First feature options" .PP \fB\-asource\fR \fIstring\fR .RS 4 By default any feature source in the feature table is allowed\&. You can set this to match any feature source you wish to allow\&. The source name is usually either the name of the program that detected the feature or it is the feature table (eg: EMBL) that the feature came from\&. The source may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to allow more than one source, separate their names with the character \*(Aq|\*(Aq, eg: gene* | embl Default value: * .RE .PP \fB\-atype\fR \fIstring\fR .RS 4 By default every feature in the feature table is allowed\&. You can set this to be any feature type you wish to allow\&. See http://www\&.ebi\&.ac\&.uk/embl/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www\&.expasy\&.org/sprot/userman\&.html for a list of the Swissprot feature types\&. The type may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to allow more than one type, separate their names with the character \*(Aq|\*(Aq, eg: *UTR | intron Default value: * .RE .PP \fB\-asense\fR \fIlist\fR .RS 4 By default any feature sense is allowed\&. You can set this to match the required sense\&. .RE .PP \fB\-aminscore\fR \fIfloat\fR .RS 4 If this is greater than or equal to the maximum score, then any score is allowed\&. Default value: 0\&.0 .RE .PP \fB\-amaxscore\fR \fIfloat\fR .RS 4 If this is less than or equal to the maximum score, then any score is permitted\&. Default value: 0\&.0 .RE .PP \fB\-atag\fR \fIstring\fR .RS 4 Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \*(AqCDS\*(Aq type of feature may have the tags \*(Aq/codon\*(Aq, \*(Aq/codon_start\*(Aq, \*(Aq/db_xref\*(Aq, \*(Aq/EC_number\*(Aq, \*(Aq/evidence\*(Aq, \*(Aq/exception\*(Aq, \*(Aq/function\*(Aq, \*(Aq/gene\*(Aq, \*(Aq/label\*(Aq, \*(Aq/map\*(Aq, \*(Aq/note\*(Aq, \*(Aq/number\*(Aq, \*(Aq/partial\*(Aq, \*(Aq/product\*(Aq, \*(Aq/protein_id\*(Aq, \*(Aq/pseudo\*(Aq, \*(Aq/standard_name\*(Aq, \*(Aq/translation\*(Aq, \*(Aq/transl_except\*(Aq, \*(Aq/transl_table\*(Aq, or \*(Aq/usedin\*(Aq\&. Some of these tags also have values, for example \*(Aq/gene\*(Aq can have the value of the gene name\&. By default any feature tag in the feature table is allowed\&. You can set this to match any feature tag you wish to allow\&. The tag may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to allow more than one tag, separate their names with the character \*(Aq|\*(Aq, eg: gene | label Default value: * .RE .PP \fB\-avalue\fR \fIstring\fR .RS 4 Tag values are the values associated with a feature tag\&. Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \*(AqCDS\*(Aq type of feature may have the tags \*(Aq/codon\*(Aq, \*(Aq/codon_start\*(Aq, \*(Aq/db_xref\*(Aq, \*(Aq/EC_number\*(Aq, \*(Aq/evidence\*(Aq, \*(Aq/exception\*(Aq, \*(Aq/function\*(Aq, \*(Aq/gene\*(Aq, \*(Aq/label\*(Aq, \*(Aq/map\*(Aq, \*(Aq/note\*(Aq, \*(Aq/number\*(Aq, \*(Aq/partial\*(Aq, \*(Aq/product\*(Aq, \*(Aq/protein_id\*(Aq, \*(Aq/pseudo\*(Aq, \*(Aq/standard_name\*(Aq, \*(Aq/translation\*(Aq, \*(Aq/transl_except\*(Aq, \*(Aq/transl_table\*(Aq, or \*(Aq/usedin\*(Aq\&. Only some of these tags can have values, for example \*(Aq/gene\*(Aq can have the value of the gene name\&. By default any feature tag value in the feature table is allowed\&. You can set this to match any feature tag value you wish to allow\&. The tag value may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to allow more than one tag value, separate their names with the character \*(Aq|\*(Aq, eg: pax* | 10 Default value: * .RE .SS "Second feature options" .PP \fB\-bsource\fR \fIstring\fR .RS 4 By default any feature source in the feature table is allowed\&. You can set this to match any feature source you wish to allow\&. The source name is usually either the name of the program that detected the feature or it is the feature table (eg: EMBL) that the feature came from\&. The source may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to allow more than one source, separate their names with the character \*(Aq|\*(Aq, eg: gene* | embl Default value: * .RE .PP \fB\-btype\fR \fIstring\fR .RS 4 By default every feature in the feature table is allowed\&. You can set this to be any feature type you wish to allow\&. See http://www\&.ebi\&.ac\&.uk/embl/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www\&.expasy\&.org/sprot/userman\&.html for a list of the Swissprot feature types\&. The type may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to allow more than one type, separate their names with the character \*(Aq|\*(Aq, eg: *UTR | intron Default value: * .RE .PP \fB\-bsense\fR \fIlist\fR .RS 4 By default any feature sense is allowed\&. You can set this to match the required sense\&. .RE .PP \fB\-bminscore\fR \fIfloat\fR .RS 4 If this is greater than or equal to the maximum score, then any score is allowed\&. Default value: 0\&.0 .RE .PP \fB\-bmaxscore\fR \fIfloat\fR .RS 4 If this is less than or equal to the maximum score, then any score is permitted\&. Default value: 0\&.0 .RE .PP \fB\-btag\fR \fIstring\fR .RS 4 Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \*(AqCDS\*(Aq type of feature may have the tags \*(Aq/codon\*(Aq, \*(Aq/codon_start\*(Aq, \*(Aq/db_xref\*(Aq, \*(Aq/EC_number\*(Aq, \*(Aq/evidence\*(Aq, \*(Aq/exception\*(Aq, \*(Aq/function\*(Aq, \*(Aq/gene\*(Aq, \*(Aq/label\*(Aq, \*(Aq/map\*(Aq, \*(Aq/note\*(Aq, \*(Aq/number\*(Aq, \*(Aq/partial\*(Aq, \*(Aq/product\*(Aq, \*(Aq/protein_id\*(Aq, \*(Aq/pseudo\*(Aq, \*(Aq/standard_name\*(Aq, \*(Aq/translation\*(Aq, \*(Aq/transl_except\*(Aq, \*(Aq/transl_table\*(Aq, or \*(Aq/usedin\*(Aq\&. Some of these tags also have values, for example \*(Aq/gene\*(Aq can have the value of the gene name\&. By default any feature tag in the feature table is allowed\&. You can set this to match any feature tag you wish to allow\&. The tag may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to allow more than one tag, separate their names with the character \*(Aq|\*(Aq, eg: gene | label Default value: * .RE .PP \fB\-bvalue\fR \fIstring\fR .RS 4 Tag values are the values associated with a feature tag\&. Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \*(AqCDS\*(Aq type of feature may have the tags \*(Aq/codon\*(Aq, \*(Aq/codon_start\*(Aq, \*(Aq/db_xref\*(Aq, \*(Aq/EC_number\*(Aq, \*(Aq/evidence\*(Aq, \*(Aq/exception\*(Aq, \*(Aq/function\*(Aq, \*(Aq/gene\*(Aq, \*(Aq/label\*(Aq, \*(Aq/map\*(Aq, \*(Aq/note\*(Aq, \*(Aq/number\*(Aq, \*(Aq/partial\*(Aq, \*(Aq/product\*(Aq, \*(Aq/protein_id\*(Aq, \*(Aq/pseudo\*(Aq, \*(Aq/standard_name\*(Aq, \*(Aq/translation\*(Aq, \*(Aq/transl_except\*(Aq, \*(Aq/transl_table\*(Aq, or \*(Aq/usedin\*(Aq\&. Only some of these tags can have values, for example \*(Aq/gene\*(Aq can have the value of the gene name\&. By default any feature tag value in the feature table is allowed\&. You can set this to match any feature tag value you wish to allow\&. The tag value may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to allow more than one tag value, separate their names with the character \*(Aq|\*(Aq, eg: pax* | 10 Default value: * .RE .SS "Feature relation options" .PP \fB\-overlap\fR \fIlist\fR .RS 4 This allows you to specify the allowed overlaps of the features A and B\&. You can allow any or no overlaps, specify that they must or must not overlap, that one must or must not be wholly enclosed within another feature\&. Default value: A .RE .PP \fB\-minrange\fR \fIinteger\fR .RS 4 If this is greater or equal to \*(Aqmaxrange\*(Aq, then no min or max range is specified .RE .PP \fB\-maxrange\fR \fIinteger\fR .RS 4 If this is less than or equal to \*(Aqminrange\*(Aq, then no min or max range is specified .RE .PP \fB\-rangetype\fR \fIlist\fR .RS 4 This allows you to specify the positions from which the allowed minimum or maximum distance between the features is measured Default value: N .RE .PP \fB\-sense\fR \fIlist\fR .RS 4 This allows you to specify the required sense that the two features must be on\&. This is ignored (always \*(AqAny\*(Aq) when looking at protein sequence features\&. Default value: A .RE .PP \fB\-order\fR \fIlist\fR .RS 4 This allows you to specify the required order of the two features\&. The order is measured from the start positions of the features\&. This criterion is always applied despite the specified overlap type required\&. Default value: A .RE .SS "Output section" .PP \fB\-twoout\fR \fItoggle\fR .RS 4 If you set this to be true, then the two features themselves will be written out\&. If it is left as false, then a single feature will be written out covering the two features you found\&. Default value: N .RE .PP \fB\-typeout\fR \fIstring\fR .RS 4 If you have specified that the pairs of features that are found should be reported as one feature in the ouput, then you can specify the \*(Aqtype\*(Aq name of the new feature here\&. By default every feature in the feature table is allowed\&. See http://www\&.ebi\&.ac\&.uk/embl/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www\&.expasy\&.org/sprot/userman\&.html for a list of the Swissprot feature types\&. If you specify an invalid feature type name, then the default name \*(Aqmisc_feature\*(Aq is used\&. Default value: misc_feature .RE .PP \fB\-outfile\fR \fIreport\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP twofeat is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/dotmatcher.1e0000644000000000000000000000654212214054043013344 0ustar '\" t .\" Title: DOTMATCHER .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DOTMATCHER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" dotmatcher \- Draw a threshold dotplot of two sequences .SH "SYNOPSIS" .HP \w'\fBdotmatcher\fR\ 'u \fBdotmatcher\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR [\fB\-matrixfile\ \fR\fB\fImatrix\fR\fR] [\fB\-windowsize\ \fR\fB\fIinteger\fR\fR] [\fB\-threshold\ \fR\fB\fIinteger\fR\fR] \fB\-stretch\ \fR\fB\fItoggle\fR\fR \fB\-graph\ \fR\fB\fIgraph\fR\fR \fB\-xygraph\ \fR\fB\fIxygraph\fR\fR .HP \w'\fBdotmatcher\fR\ 'u \fBdotmatcher\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdotmatcher\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Dot plots" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-asequence\fR \fIsequence\fR .RS 4 .RE .PP \fB\-bsequence\fR \fIsequence\fR .RS 4 .RE .PP \fB\-matrixfile\fR \fImatrix\fR .RS 4 This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&. .RE .SS "Additional section" .PP \fB\-windowsize\fR \fIinteger\fR .RS 4 Default value: 10 .RE .PP \fB\-threshold\fR \fIinteger\fR .RS 4 Default value: 23 .RE .SS "Output section" .PP \fB\-stretch\fR \fItoggle\fR .RS 4 Display a non\-proportional graph Default value: N .RE .PP \fB\-graph\fR \fIgraph\fR .RS 4 .RE .PP \fB\-xygraph\fR \fIxygraph\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP dotmatcher is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/ajbad.1e0000644000000000000000000000616312214054043012252 0ustar '\" t .\" Title: AJBAD .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "AJBAD" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" ajbad \- Test file for ACD parsing .SH "SYNOPSIS" .HP \w'\fBajbad\fR\ 'u \fBajbad\fR \fB\-typea\ \fR\fB\fIstring\fR\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR \fB\-eco\ \fR\fB\fIcodon\fR\fR \fB\-typeb\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-a\ \fR\fB\fIinteger\fR\fR \fB\-b\ \fR\fB\fIinteger\fR\fR \fB\-c\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBajbad\fR\ 'u \fBajbad\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBajbad\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Test" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-typea\fR \fIstring\fR .RS 4 .RE .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .PP \fB\-bsequence\fR \fIsequence\fR .RS 4 .RE .PP \fB\-eco\fR \fIcodon\fR .RS 4 .RE .SS "Required section" .PP \fB\-typeb\fR \fIstring\fR .RS 4 Default value: $(seqa\&.type) .RE .PP \fB\-date\fR \fIstring\fR .RS 4 Default value: 00/00/00 .RE .SS "Advanced section" .PP \fB\-a\fR \fIinteger\fR .RS 4 .RE .PP \fB\-b\fR \fIinteger\fR .RS 4 Default value: 15 .RE .PP \fB\-c\fR \fIfloat\fR .RS 4 Default value: 1\&.6 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP ajbad is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/codcopy.1e0000644000000000000000000000476212214054043012654 0ustar '\" t .\" Title: CODCOPY .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "CODCOPY" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" codcopy \- Copy and reformat a codon usage table .SH "SYNOPSIS" .HP \w'\fBcodcopy\fR\ 'u \fBcodcopy\fR \fB\-infile\ \fR\fB\fIcodon\fR\fR \fB\-outfile\ \fR\fB\fIoutcodon\fR\fR .HP \w'\fBcodcopy\fR\ 'u \fBcodcopy\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBcodcopy\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval,Nucleic:Codon usage,Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIcodon\fR .RS 4 .RE .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutcodon\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP codcopy is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/dbxstat.1e0000644000000000000000000000554012214054043012660 0ustar '\" t .\" Title: DBXSTAT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DBXSTAT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" dbxstat \- Dump statistics for dbx databases .SH "SYNOPSIS" .HP \w'\fBdbxstat\fR\ 'u \fBdbxstat\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-field\ \fR\fB\fIstring\fR\fR \fB\-indexdir\ \fR\fB\fIdirectory\fR\fR \fB\-minimum\ \fR\fB\fIinteger\fR\fR \fB\-maximum\ \fR\fB\fIinteger\fR\fR \fB\-$(dbname)\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBdbxstat\fR\ 'u \fBdbxstat\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdbxstat\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-dbname\fR \fIstring\fR .RS 4 .RE .PP \fB\-field\fR \fIstring\fR .RS 4 Default value: id .RE .PP \fB\-indexdir\fR \fIdirectory\fR .RS 4 .RE .SS "Required section" .SS "Advanced section" .PP \fB\-minimum\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-maximum\fR \fIinteger\fR .RS 4 .RE .SS "Output section" .PP \fB\-$(dbname)\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP dbxstat is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/entrytax.1e0000644000000000000000000000515612214054043013070 0ustar '\" t .\" Title: ENTRYTAX .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ENTRYTAX" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" entrytax \- Identify and retrieve sequence entries containing taxonomy IDs .SH "SYNOPSIS" .HP \w'\fBentrytax\fR\ 'u \fBentrytax\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-ids\ \fR\fB\fIstring\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBentrytax\fR\ 'u \fBentrytax\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBentrytax\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-ids\fR \fIstring\fR .RS 4 .RE .SS "Required section" .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP entrytax is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/octanol.1e0000644000000000000000000000602412214054043012644 0ustar '\" t .\" Title: OCTANOL .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "OCTANOL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" octanol \- Draw a White\-Wimley protein hydropathy plot .SH "SYNOPSIS" .HP \w'\fBoctanol\fR\ 'u \fBoctanol\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-datafile\ \fR\fB\fIdatafile\fR\fR] [\fB\-width\ \fR\fB\fIinteger\fR\fR] \fB\-graph\ \fR\fB\fIxygraph\fR\fR [\fB\-plotoctanol\ \fR\fB\fIboolean\fR\fR] [\fB\-plotinterface\ \fR\fB\fIboolean\fR\fR] [\fB\-plotdifference\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBoctanol\fR\ 'u \fBoctanol\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBoctanol\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Properties" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .PP \fB\-datafile\fR \fIdatafile\fR .RS 4 Default value: Ewhite\-wimley\&.dat .RE .SS "Additional section" .PP \fB\-width\fR \fIinteger\fR .RS 4 Default value: 19 .RE .SS "Output section" .PP \fB\-graph\fR \fIxygraph\fR .RS 4 .RE .PP \fB\-plotoctanol\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-plotinterface\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-plotdifference\fR \fIboolean\fR .RS 4 Default value: Y .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP octanol is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/tcode.1e0000644000000000000000000000736712214054043012316 0ustar '\" t .\" Title: TCODE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "TCODE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" tcode \- Identify protein\-coding regions using Fickett TESTCODE statistic .SH "SYNOPSIS" .HP \w'\fBtcode\fR\ 'u \fBtcode\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-datafile\ \fR\fB\fIdatafile\fR\fR \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-step\ \fR\fB\fIinteger\fR\fR \fB\-plot\ \fR\fB\fItoggle\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR .HP \w'\fBtcode\fR\ 'u \fBtcode\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBtcode\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Gene finding" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-datafile\fR \fIdatafile\fR .RS 4 The default data file is Etcode\&.dat and contains coding probabilities for each base\&. The probabilities are for both positional and compositional information\&. Default value: Etcode\&.dat .RE .SS "Required section" .PP \fB\-window\fR \fIinteger\fR .RS 4 This is the number of nucleotide bases over which the TESTCODE statistic will be performed each time\&. The window will then slide along the sequence, covering the same number of bases each time\&. Default value: 200 .RE .SS "Advanced section" .PP \fB\-step\fR \fIinteger\fR .RS 4 The selected window will, by default, slide along the nucleotide sequence by three bases at a time, retaining the frame (although the algorithm is not frame sensitive)\&. This may be altered to increase or decrease the increment of the slide\&. Default value: 3 .RE .SS "Output section" .PP \fB\-plot\fR \fItoggle\fR .RS 4 On selection a graph of the sequence (X axis) plotted against the coding score (Y axis) will be displayed\&. Sequence above the green line is coding, that below the red line is non\-coding\&. Default value: N .RE .PP \fB\-outfile\fR \fIreport\fR .RS 4 .RE .PP \fB\-graph\fR \fIxygraph\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP tcode is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/palindrome.1e0000644000000000000000000000577012214054043013346 0ustar '\" t .\" Title: PALINDROME .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PALINDROME" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" palindrome \- Finds inverted repeats in nucleotide sequence(s) .SH "SYNOPSIS" .HP \w'\fBpalindrome\fR\ 'u \fBpalindrome\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-minpallen\ \fR\fB\fIinteger\fR\fR \fB\-maxpallen\ \fR\fB\fIinteger\fR\fR \fB\-gaplimit\ \fR\fB\fIinteger\fR\fR \fB\-nummismatches\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-overlap\ \fR\fB\fIboolean\fR\fR .HP \w'\fBpalindrome\fR\ 'u \fBpalindrome\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBpalindrome\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Repeats" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Required section" .PP \fB\-minpallen\fR \fIinteger\fR .RS 4 Default value: 10 .RE .PP \fB\-maxpallen\fR \fIinteger\fR .RS 4 Default value: 100 .RE .PP \fB\-gaplimit\fR \fIinteger\fR .RS 4 Default value: 100 .RE .PP \fB\-nummismatches\fR \fIinteger\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-overlap\fR \fIboolean\fR .RS 4 Default value: Y .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP palindrome is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/intconv.1e0000644000000000000000000000467612214054043012700 0ustar '\" t .\" Title: INTCONV .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "INTCONV" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" intconv \- Convert ints to ajints and longs to ajlongs .SH "SYNOPSIS" .HP \w'\fBintconv\fR\ 'u \fBintconv\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBintconv\fR\ 'u \fBintconv\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBintconv\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Test" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP intconv is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/backtranseq.1e0000644000000000000000000000520412214054043013502 0ustar '\" t .\" Title: BACKTRANSEQ .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "BACKTRANSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" backtranseq \- Back\-translate a protein sequence to a nucleotide sequence .SH "SYNOPSIS" .HP \w'\fBbacktranseq\fR\ 'u \fBbacktranseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-cfile\ \fR\fB\fIcodon\fR\fR] \fB\-outfile\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBbacktranseq\fR\ 'u \fBbacktranseq\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBbacktranseq\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Translation,Protein:Composition" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-cfile\fR \fIcodon\fR .RS 4 Default value: Ehuman\&.cut .RE .SS "Output section" .PP \fB\-outfile\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP backtranseq is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/ajfeatest.1e0000644000000000000000000000473712214054043013164 0ustar '\" t .\" Title: AJFEATEST .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "AJFEATEST" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" ajfeatest \- Reads and writes (returns) a sequence and its features .SH "SYNOPSIS" .HP \w'\fBajfeatest\fR\ 'u \fBajfeatest\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR .HP \w'\fBajfeatest\fR\ 'u \fBajfeatest\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBajfeatest\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Test" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqout\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP ajfeatest is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/lindna.1e0000644000000000000000000001221312214054043012447 0ustar '\" t .\" Title: LINDNA .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "LINDNA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" lindna \- Draws linear maps of DNA constructs .SH "SYNOPSIS" .HP \w'\fBlindna\fR\ 'u \fBlindna\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR [\fB\-maxgroups\ \fR\fB\fIinteger\fR\fR] [\fB\-maxlabels\ \fR\fB\fIinteger\fR\fR] \fB\-ruler\ \fR\fB\fIboolean\fR\fR \fB\-blocktype\ \fR\fB\fIlist\fR\fR [\fB\-intersymbol\ \fR\fB\fIselection\fR\fR] [\fB\-intercolour\ \fR\fB\fIinteger\fR\fR] [\fB\-interticks\ \fR\fB\fIboolean\fR\fR] [\fB\-gapsize\ \fR\fB\fIinteger\fR\fR] [\fB\-ticklines\ \fR\fB\fIboolean\fR\fR] [\fB\-textheight\ \fR\fB\fIfloat\fR\fR] [\fB\-textlength\ \fR\fB\fIfloat\fR\fR] [\fB\-margin\ \fR\fB\fIfloat\fR\fR] [\fB\-tickheight\ \fR\fB\fIfloat\fR\fR] [\fB\-blockheight\ \fR\fB\fIfloat\fR\fR] [\fB\-rangeheight\ \fR\fB\fIfloat\fR\fR] [\fB\-gapgroup\ \fR\fB\fIfloat\fR\fR] [\fB\-postext\ \fR\fB\fIfloat\fR\fR] \fB\-graphout\ \fR\fB\fIgraph\fR\fR .HP \w'\fBlindna\fR\ 'u \fBlindna\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBlindna\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Display" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIinfile\fR .RS 4 Default value: inputfile .RE .SS "Additional section" .PP \fB\-maxgroups\fR \fIinteger\fR .RS 4 Default value: 20 .RE .PP \fB\-maxlabels\fR \fIinteger\fR .RS 4 Default value: 10000 .RE .SS "Output section" .PP \fB\-ruler\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-blocktype\fR \fIlist\fR .RS 4 Default value: Filled .RE .PP \fB\-intersymbol\fR \fIselection\fR .RS 4 Default value: Straight .RE .PP \fB\-intercolour\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-interticks\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-gapsize\fR \fIinteger\fR .RS 4 A zero value allows the application to choose a gap size .RE .PP \fB\-ticklines\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-textheight\fR \fIfloat\fR .RS 4 Height of text\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1\&.0 .RE .PP \fB\-textlength\fR \fIfloat\fR .RS 4 Length of text\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1\&.0 .RE .PP \fB\-margin\fR \fIfloat\fR .RS 4 Width of left margin\&. This is the region left to the groups where the names of the groups are displayed\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1\&.0 .RE .PP \fB\-tickheight\fR \fIfloat\fR .RS 4 Height of ticks\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1\&.0 .RE .PP \fB\-blockheight\fR \fIfloat\fR .RS 4 Height of blocks\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1 .RE .PP \fB\-rangeheight\fR \fIfloat\fR .RS 4 Height of range ends\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1\&.0 .RE .PP \fB\-gapgroup\fR \fIfloat\fR .RS 4 Space between groups\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1\&.0 .RE .PP \fB\-postext\fR \fIfloat\fR .RS 4 Space between text and ticks, blocks, and ranges\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1\&.0 .RE .PP \fB\-graphout\fR \fIgraph\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP lindna is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/showfeat.1e0000644000000000000000000002573712214054043013041 0ustar '\" t .\" Title: SHOWFEAT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SHOWFEAT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" showfeat \- Display features of a sequence in pretty format .SH "SYNOPSIS" .HP \w'\fBshowfeat\fR\ 'u \fBshowfeat\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-sourcematch\ \fR\fB\fIstring\fR\fR] [\fB\-typematch\ \fR\fB\fIstring\fR\fR] [\fB\-tagmatch\ \fR\fB\fIstring\fR\fR] [\fB\-valuematch\ \fR\fB\fIstring\fR\fR] [\fB\-sort\ \fR\fB\fIlist\fR\fR] [\fB\-joinfeatures\ \fR\fB\fIboolean\fR\fR] [\fB\-annotation\ \fR\fB\fIrange\fR\fR] \fB\-html\ \fR\fB\fIboolean\fR\fR \fB\-id\ \fR\fB\fIboolean\fR\fR \fB\-description\ \fR\fB\fIboolean\fR\fR \fB\-scale\ \fR\fB\fIboolean\fR\fR \fB\-width\ \fR\fB\fIinteger\fR\fR \fB\-collapse\ \fR\fB\fIboolean\fR\fR \fB\-forward\ \fR\fB\fIboolean\fR\fR \fB\-reverse\ \fR\fB\fIboolean\fR\fR \fB\-unknown\ \fR\fB\fIboolean\fR\fR \fB\-strand\ \fR\fB\fIboolean\fR\fR \fB\-origin\ \fR\fB\fIboolean\fR\fR \fB\-position\ \fR\fB\fIboolean\fR\fR \fB\-type\ \fR\fB\fIboolean\fR\fR \fB\-tags\ \fR\fB\fIboolean\fR\fR \fB\-values\ \fR\fB\fIboolean\fR\fR \fB\-stricttags\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBshowfeat\fR\ 'u \fBshowfeat\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBshowfeat\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Display,Feature tables" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Additional section" .PP \fB\-sourcematch\fR \fIstring\fR .RS 4 By default any feature source in the feature table is shown\&. You can set this to match any feature source you wish to show\&. The source name is usually either the name of the program that detected the feature or it is the feature table (eg: EMBL) that the feature came from\&. The source may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one source, separate their names with the character \*(Aq|\*(Aq, eg: gene* | embl Default value: * .RE .PP \fB\-typematch\fR \fIstring\fR .RS 4 By default any feature type in the feature table is shown\&. You can set this to match any feature type you wish to show\&. See http://www\&.ebi\&.ac\&.uk/embl/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www\&.expasy\&.org/sprot/userman\&.html for a list of the Swissprot feature types\&. The type may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one type, separate their names with the character \*(Aq|\*(Aq, eg: *UTR | intron Default value: * .RE .PP \fB\-tagmatch\fR \fIstring\fR .RS 4 Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \*(AqCDS\*(Aq type of feature may have the tags \*(Aq/codon\*(Aq, \*(Aq/codon_start\*(Aq, \*(Aq/db_xref\*(Aq, \*(Aq/EC_number\*(Aq, \*(Aq/evidence\*(Aq, \*(Aq/exception\*(Aq, \*(Aq/function\*(Aq, \*(Aq/gene\*(Aq, \*(Aq/label\*(Aq, \*(Aq/map\*(Aq, \*(Aq/note\*(Aq, \*(Aq/number\*(Aq, \*(Aq/partial\*(Aq, \*(Aq/product\*(Aq, \*(Aq/protein_id\*(Aq, \*(Aq/pseudo\*(Aq, \*(Aq/standard_name\*(Aq, \*(Aq/translation\*(Aq, \*(Aq/transl_except\*(Aq, \*(Aq/transl_table\*(Aq, or \*(Aq/usedin\*(Aq\&. Some of these tags also have values, for example \*(Aq/gene\*(Aq can have the value of the gene name\&. By default any feature tag in the feature table is shown\&. You can set this to match any feature tag you wish to show\&. The tag may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one tag, separate their names with the character \*(Aq|\*(Aq, eg: gene | label Default value: * .RE .PP \fB\-valuematch\fR \fIstring\fR .RS 4 Tag values are the values associated with a feature tag\&. Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \*(AqCDS\*(Aq type of feature may have the tags \*(Aq/codon\*(Aq, \*(Aq/codon_start\*(Aq, \*(Aq/db_xref\*(Aq, \*(Aq/EC_number\*(Aq, \*(Aq/evidence\*(Aq, \*(Aq/exception\*(Aq, \*(Aq/function\*(Aq, \*(Aq/gene\*(Aq, \*(Aq/label\*(Aq, \*(Aq/map\*(Aq, \*(Aq/note\*(Aq, \*(Aq/number\*(Aq, \*(Aq/partial\*(Aq, \*(Aq/product\*(Aq, \*(Aq/protein_id\*(Aq, \*(Aq/pseudo\*(Aq, \*(Aq/standard_name\*(Aq, \*(Aq/translation\*(Aq, \*(Aq/transl_except\*(Aq, \*(Aq/transl_table\*(Aq, or \*(Aq/usedin\*(Aq\&. Only some of these tags can have values, for example \*(Aq/gene\*(Aq can have the value of the gene name\&. By default any feature tag value in the feature table is shown\&. You can set this to match any feature tag value you wish to show\&. The tag value may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one tag value, separate their names with the character \*(Aq|\*(Aq, eg: pax* | 10 Default value: * .RE .PP \fB\-sort\fR \fIlist\fR .RS 4 Default value: start .RE .PP \fB\-joinfeatures\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-annotation\fR \fIrange\fR .RS 4 Regions to annotate by marking\&. If this is left blank, then no annotation is added\&. A set of regions is specified by a set of pairs of positions followed by optional text\&. The positions are integers\&. They are followed by any text (but not digits when on the command\-line)\&. Examples of region specifications are: 24\-45 new domain 56\-78 match to Mouse 1\-100 First part 120\-156 oligo A file of ranges to annotate (one range per line) can be specified as \*(Aq@filename\*(Aq\&. .RE .SS "Advanced section" .PP \fB\-html\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-id\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to display the ID name of the sequence\&. Default value: Y .RE .PP \fB\-description\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to display the description of the sequence\&. Default value: Y .RE .PP \fB\-scale\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to display the scale line\&. Default value: Y .RE .PP \fB\-width\fR \fIinteger\fR .RS 4 You can expand (or contract) the width of the ASCII\-character graphics display of the positions of the features using this value\&. For example, a width of 80 characters would cover a standard page width and a width a 10 characters would be nearly unreadable\&. If the width is set to less than 4, the graphics lines and the scale line will not be displayed\&. Default value: 60 .RE .PP \fB\-collapse\fR \fIboolean\fR .RS 4 If this is set, then features from the same source and of the same type and sense are all printed on the same line\&. For instance if there are several features from the EMBL feature table (ie\&. the same source) which are all of type \*(Aqexon\*(Aq in the same sense, then they will all be displayed on the same line\&. This makes it hard to distinguish overlapping features\&. If this is set to false then each feature is displayed on a separate line making it easier to distinguish where features start and end\&. Default value: N .RE .PP \fB\-forward\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to display forward sense features\&. Default value: Y .RE .PP \fB\-reverse\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to display reverse sense features\&. Default value: Y .RE .PP \fB\-unknown\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to display unknown sense features\&. (ie\&. features with no directionality \- all protein features are of this type and some nucleic features (for example, CG\-rich regions))\&. Default value: Y .RE .PP \fB\-strand\fR \fIboolean\fR .RS 4 Set this if you wish to display the strand of the features\&. Protein features are always directionless (indicated by \*(Aq0\*(Aq), forward is indicated by \*(Aq+\*(Aq and reverse is \*(Aq\-\*(Aq\&. Default value: N .RE .PP \fB\-origin\fR \fIboolean\fR .RS 4 Set this if you wish to display the origin of the features\&. The source name is usually either the name of the program that detected the feature or it is the name of the feature table (eg: EMBL) that the feature came from\&. Default value: N .RE .PP \fB\-position\fR \fIboolean\fR .RS 4 Set this if you wish to display the start and end position of the features\&. If several features are being displayed on the same line, then the start and end positions will be joined by a comma, for example: \*(Aq189\-189,225\-225\*(Aq\&. Default value: N .RE .PP \fB\-type\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to display the type of the features\&. Default value: Y .RE .PP \fB\-tags\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to display the tags and values of the features\&. Default value: N .RE .PP \fB\-values\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to display the tag values of the features\&. If this is set to be false, only the tag names will be displayed\&. If the tags are not displayed, then the values will not be displayed\&. The value of the \*(Aqtranslation\*(Aq tag is never displayed as it is often extremely long\&. Default value: Y .RE .PP \fB\-stricttags\fR \fIboolean\fR .RS 4 By default if any tag/value pair in a feature matches the specified tag and value, then all the tags/value pairs of that feature will be displayed\&. If this is set to be true, then only those tag/value pairs in a feature that match the specified tag and value will be displayed\&. Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP showfeat is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/feattext.1e0000644000000000000000000000471012214054043013031 0ustar '\" t .\" Title: FEATTEXT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "FEATTEXT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" feattext \- Return a feature table original text .SH "SYNOPSIS" .HP \w'\fBfeattext\fR\ 'u \fBfeattext\fR \fB\-features\ \fR\fB\fIfeatures\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBfeattext\fR\ 'u \fBfeattext\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfeattext\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-features\fR \fIfeatures\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP feattext is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/descseq.1e0000644000000000000000000000557712214054043012650 0ustar '\" t .\" Title: DESCSEQ .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DESCSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" descseq \- Alter the name or description of a sequence\&. .SH "SYNOPSIS" .HP \w'\fBdescseq\fR\ 'u \fBdescseq\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-name\ \fR\fB\fIstring\fR\fR] [\fB\-description\ \fR\fB\fIstring\fR\fR] \fB\-append\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR .HP \w'\fBdescseq\fR\ 'u \fBdescseq\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdescseq\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .SS "Additional section" .PP \fB\-name\fR \fIstring\fR .RS 4 .RE .PP \fB\-description\fR \fIstring\fR .RS 4 .RE .SS "Advanced section" .PP \fB\-append\fR \fIboolean\fR .RS 4 This allows you to append the name or description you have given on to the end of the existing name or description of the sequence\&. Default value: N .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqout\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP descseq is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/taxgetup.1e0000644000000000000000000000512012214054043013042 0ustar '\" t .\" Title: TAXGETUP .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "TAXGETUP" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" taxgetup \- Get parents of taxon(s) .SH "SYNOPSIS" .HP \w'\fBtaxgetup\fR\ 'u \fBtaxgetup\fR \fB\-taxons\ \fR\fB\fItaxon\fR\fR \fB\-hidden\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIouttaxon\fR\fR .HP \w'\fBtaxgetup\fR\ 'u \fBtaxgetup\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBtaxgetup\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:Taxonomy" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-taxons\fR \fItaxon\fR .RS 4 .RE .SS "Additional section" .SS "Advanced section" .PP \fB\-hidden\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIouttaxon\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP taxgetup is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/cachedas.1e0000644000000000000000000000607512214054043012746 0ustar '\" t .\" Title: CACHEDAS .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "CACHEDAS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" cachedas \- Generates server cache file for DAS servers or for the DAS registry .SH "SYNOPSIS" .HP \w'\fBcachedas\fR\ 'u \fBcachedas\fR [\fB\-sequencesourcesonly\ \fR\fB\fIboolean\fR\fR] \fB\-host\ \fR\fB\fIstring\fR\fR \fB\-path\ \fR\fB\fIstring\fR\fR \fB\-port\ \fR\fB\fIinteger\fR\fR \fB\-servername\ \fR\fB\fIstring\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] \fB\-cachefile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBcachedas\fR\ 'u \fBcachedas\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBcachedas\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data resources" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequencesourcesonly\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-host\fR \fIstring\fR .RS 4 Default value: www\&.dasregistry\&.org .RE .PP \fB\-path\fR \fIstring\fR .RS 4 Default value: /das .RE .PP \fB\-port\fR \fIinteger\fR .RS 4 Default value: 80 .RE .PP \fB\-servername\fR \fIstring\fR .RS 4 Default value: das .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .PP \fB\-cachefile\fR \fIoutfile\fR .RS 4 Default value: server\&.$(servername) .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP cachedas is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/texttoxml.1e0000644000000000000000000000621212214054043013254 0ustar '\" t .\" Title: TEXTTOXML .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "TEXTTOXML" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" texttoxml \- Convert a plain text format to an XML format .SH "SYNOPSIS" .HP \w'\fBtexttoxml\fR\ 'u \fBtexttoxml\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-type\ \fR\fB\fIlist\fR\fR \fB\-seq\ \fR\fB\fIlist\fR\fR \fB\-feat\ \fR\fB\fIlist\fR\fR \fB\-align\ \fR\fB\fIlist\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBtexttoxml\fR\ 'u \fBtexttoxml\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBtexttoxml\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Misc" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .SS "Required section" .PP \fB\-type\fR \fIlist\fR .RS 4 You must specify the type of file content so that appropriate output format options may be generated\&. .RE .PP \fB\-seq\fR \fIlist\fR .RS 4 This option sets the format of a sequence output file\&. Default value: X .RE .PP \fB\-feat\fR \fIlist\fR .RS 4 This option sets the format of a sequence feature output file\&. Default value: X .RE .PP \fB\-align\fR \fIlist\fR .RS 4 This option sets the format of a sequence alignment output file\&. Default value: X .RE .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP texttoxml is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/seqgo.1e0000644000000000000000000000547012214054043012327 0ustar '\" t .\" Title: SEQGO .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SEQGO" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" seqgo \- Extract a list of GO terms from a sequence entry .SH "SYNOPSIS" .HP \w'\fBseqgo\fR\ 'u \fBseqgo\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-html\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBseqgo\fR\ 'u \fBseqgo\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBseqgo\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:GO" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .SS "Required section" .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 This is the file of GO ontology terms that were found in the input sequnce entry\&. .RE .SS "Html section" .PP \fB\-html\fR \fIboolean\fR .RS 4 If you are sending the output to a file, this will format it for displaying as a table in a WWW document\&. Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP seqgo is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fuzznuc.1e0000644000000000000000000000743512214054043012720 0ustar '\" t .\" Title: FUZZNUC .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "FUZZNUC" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fuzznuc \- Search for patterns in nucleotide sequences .SH "SYNOPSIS" .HP \w'\fBfuzznuc\fR\ 'u \fBfuzznuc\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-pattern\ \fR\fB\fIpattern\fR\fR \fB\-complement\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR .HP \w'\fBfuzznuc\fR\ 'u \fBfuzznuc\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfuzznuc\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Motifs" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-pattern\fR \fIpattern\fR .RS 4 The standard IUPAC one\-letter codes for the nucleotides are used\&. The symbol \*(Aqn\*(Aq is used for a position where any nucleotide is accepted\&. Ambiguities are indicated by listing the acceptable nucleotides for a given position, between square parentheses \*(Aq[ ]\*(Aq\&. For example: [ACG] stands for A or C or G\&. Ambiguities are also indicated by listing between a pair of curly brackets \*(Aq{ }\*(Aq the nucleotides that are not accepted at a given position\&. For example: {AG} stands for any nucleotides except A and G\&. Each element in a pattern is separated from its neighbor by a \*(Aq\-\*(Aq\&. (Optional in fuzznuc)\&. Repetition of an element of the pattern can be indicated by following that element with a numerical value or a numerical range between parenthesis\&. Examples: N(3) corresponds to N\-N\-N, N(2,4) corresponds to N\-N or N\-N\-N or N\-N\-N\-N\&. When a pattern is restricted to either the 5\*(Aq or 3\*(Aq end of a sequence, that pattern either starts with a \*(Aq<\*(Aq symbol or respectively ends with a \*(Aq>\*(Aq symbol\&. A period ends the pattern\&. (Optional in fuzznuc)\&. For example, [CG](5)TG{A}N(1,5)C .RE .SS "Advanced section" .PP \fB\-complement\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIreport\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fuzznuc is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/dbxresource.1e0000644000000000000000000000707712214054043013543 0ustar '\" t .\" Title: DBXRESOURCE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DBXRESOURCE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" dbxresource \- Index a data resource catalogue using b+tree indices .SH "SYNOPSIS" .HP \w'\fBdbxresource\fR\ 'u \fBdbxresource\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-standardname\ \fR\fB\fIstring\fR\fR \fB\-dbresource\ \fR\fB\fIstring\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-filenames\ \fR\fB\fIstring\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-compressed\ \fR\fB\fIboolean\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBdbxresource\fR\ 'u \fBdbxresource\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdbxresource\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-dbname\fR \fIstring\fR .RS 4 Default value: drcat .RE .PP \fB\-standardname\fR \fIstring\fR .RS 4 Default value: $(dbname) .RE .PP \fB\-dbresource\fR \fIstring\fR .RS 4 Default value: drcatresource .RE .PP \fB\-directory\fR \fIdirectory\fR .RS 4 Default value: \&. .RE .PP \fB\-filenames\fR \fIstring\fR .RS 4 Default value: DRCAT\&.dat .RE .SS "Required section" .PP \fB\-fields\fR \fIlist\fR .RS 4 Default value: * .RE .PP \fB\-compressed\fR \fIboolean\fR .RS 4 Default value: Y .RE .SS "Advanced section" .PP \fB\-release\fR \fIstring\fR .RS 4 Default value: 0\&.0 .RE .PP \fB\-date\fR \fIstring\fR .RS 4 Default value: 00/00/00 .RE .PP \fB\-exclude\fR \fIstring\fR .RS 4 .RE .SS "Output section" .PP \fB\-indexoutdir\fR \fIoutdir\fR .RS 4 Default value: \&. .RE .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP dbxresource is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/showseq.1e0000644000000000000000000003731312214054043012703 0ustar '\" t .\" Title: SHOWSEQ .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SHOWSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" showseq \- Displays sequences with features in pretty format .SH "SYNOPSIS" .HP \w'\fBshowseq\fR\ 'u \fBshowseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-mfile\ \fR\fB\fIdatafile\fR\fR \fB\-format\ \fR\fB\fIlist\fR\fR \fB\-things\ \fR\fB\fIlist\fR\fR [\fB\-translate\ \fR\fB\fIrange\fR\fR] [\fB\-revtranslate\ \fR\fB\fIrange\fR\fR] [\fB\-uppercase\ \fR\fB\fIrange\fR\fR] [\fB\-highlight\ \fR\fB\fIrange\fR\fR] [\fB\-annotation\ \fR\fB\fIrange\fR\fR] [\fB\-enzymes\ \fR\fB\fIstring\fR\fR] [\fB\-table\ \fR\fB\fIlist\fR\fR] [\fB\-sourcematch\ \fR\fB\fIstring\fR\fR] [\fB\-typematch\ \fR\fB\fIstring\fR\fR] [\fB\-sensematch\ \fR\fB\fIinteger\fR\fR] [\fB\-minscore\ \fR\fB\fIfloat\fR\fR] [\fB\-maxscore\ \fR\fB\fIfloat\fR\fR] [\fB\-tagmatch\ \fR\fB\fIstring\fR\fR] [\fB\-valuematch\ \fR\fB\fIstring\fR\fR] [\fB\-stricttags\ \fR\fB\fIboolean\fR\fR] \fB\-flatreformat\ \fR\fB\fIboolean\fR\fR \fB\-mincuts\ \fR\fB\fIinteger\fR\fR \fB\-maxcuts\ \fR\fB\fIinteger\fR\fR \fB\-sitelen\ \fR\fB\fIinteger\fR\fR \fB\-single\ \fR\fB\fIboolean\fR\fR \fB\-blunt\ \fR\fB\fIboolean\fR\fR \fB\-sticky\ \fR\fB\fIboolean\fR\fR \fB\-ambiguity\ \fR\fB\fIboolean\fR\fR \fB\-plasmid\ \fR\fB\fIboolean\fR\fR \fB\-methylation\ \fR\fB\fIboolean\fR\fR \fB\-commercial\ \fR\fB\fIboolean\fR\fR \fB\-limit\ \fR\fB\fIboolean\fR\fR \fB\-orfminsize\ \fR\fB\fIinteger\fR\fR \fB\-threeletter\ \fR\fB\fIboolean\fR\fR \fB\-number\ \fR\fB\fIboolean\fR\fR \fB\-width\ \fR\fB\fIinteger\fR\fR \fB\-length\ \fR\fB\fIinteger\fR\fR \fB\-margin\ \fR\fB\fIinteger\fR\fR \fB\-name\ \fR\fB\fIboolean\fR\fR \fB\-description\ \fR\fB\fIboolean\fR\fR \fB\-offset\ \fR\fB\fIinteger\fR\fR \fB\-html\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBshowseq\fR\ 'u \fBshowseq\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBshowseq\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Translation,Nucleic:Restriction" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-mfile\fR \fIdatafile\fR .RS 4 Default value: Emethylsites\&.dat .RE .SS "Required section" .PP \fB\-format\fR \fIlist\fR .RS 4 Default value: 2 .RE .PP \fB\-things\fR \fIlist\fR .RS 4 Specify a list of one or more code characters in the order in which you wish things to be displayed one above the other down the page\&. For example if you wish to see things displayed in the order: sequence, complement sequence, ticks line, frame 1 translation, blank line; then you should enter \*(AqS,C,T,1,B\*(Aq\&. Default value: B,N,T,S,A,F .RE .SS "Additional section" .PP \fB\-translate\fR \fIrange\fR .RS 4 Regions to translate (if translating)\&. If this is left blank the complete sequence is translated\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 24\-45, 56\-78 1:45, 67=99;765\&.\&.888 .RE .PP \fB\-revtranslate\fR \fIrange\fR .RS 4 Regions to translate (if translating)\&. If this is left blank the complete sequence is translated\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 78\-56, 45\-24, 888\&.\&.765, 99=67; 45:1 .RE .PP \fB\-uppercase\fR \fIrange\fR .RS 4 Regions to put in uppercase\&. If this is left blank, then the sequence case is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 24\-45, 56\-78 1:45, 67=99;765\&.\&.888 1,5,8,10,23,45,57,99 .RE .PP \fB\-highlight\fR \fIrange\fR .RS 4 Regions to colour if formatting for HTML\&. If this is left blank, then the sequence is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are followed by any valid HTML font colour\&. Examples of region specifications are: 24\-45 blue 56\-78 orange 1\-100 green 120\-156 red A file of ranges to colour (one range per line) can be specified as \*(Aq@filename\*(Aq\&. .RE .PP \fB\-annotation\fR \fIrange\fR .RS 4 Regions to annotate by marking\&. If this is left blank, then no annotation is added\&. A set of regions is specified by a set of pairs of positions followed by optional text\&. The positions are integers\&. They are followed by any text (but not digits when on the command\-line)\&. Examples of region specifications are: 24\-45 new domain 56\-78 match to Mouse 1\-100 First part 120\-156 oligo A file of ranges to annotate (one range per line) can be specified as \*(Aq@filename\*(Aq\&. .RE .PP \fB\-enzymes\fR \fIstring\fR .RS 4 The name \*(Aqall\*(Aq reads in all enzyme names from the REBASE database\&. You can specify enzymes by giving their names with commas between then, such as: \*(AqHincII,hinfI,ppiI,hindiii\*(Aq\&. The case of the names is not important\&. You can specify a file of enzyme names to read in by giving the name of the file holding the enzyme names with a \*(Aq@\*(Aq character in front of it, for example, \*(Aq@enz\&.list\*(Aq\&. Blank lines and lines starting with a hash character or \*(Aq!\*(Aq are ignored and all other lines are concatenated together with a comma character \*(Aq,\*(Aq and then treated as the list of enzymes to search for\&. An example of a file of enzyme names is: ! my enzymes HincII, ppiII ! other enzymes hindiii HinfI PpiI Default value: all .RE .PP \fB\-table\fR \fIlist\fR .RS 4 .RE .SS "Feature display options" .PP \fB\-sourcematch\fR \fIstring\fR .RS 4 By default any feature source in the feature table is shown\&. You can set this to match any feature source you wish to show\&. The source name is usually either the name of the program that detected the feature or it is the feature table (eg: EMBL) that the feature came from\&. The source may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one source, separate their names with the character \*(Aq|\*(Aq, eg: gene* | embl Default value: * .RE .PP \fB\-typematch\fR \fIstring\fR .RS 4 By default any feature type in the feature table is shown\&. You can set this to match any feature type you wish to show\&. See http://www\&.ebi\&.ac\&.uk/embl/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www\&.expasy\&.org/sprot/userman\&.html for a list of the Swissprot feature types\&. The type may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one type, separate their names with the character \*(Aq|\*(Aq, eg: *UTR | intron Default value: * .RE .PP \fB\-sensematch\fR \fIinteger\fR .RS 4 By default any feature type in the feature table is shown\&. You can set this to match any feature sense you wish to show\&. 0 \- any sense, 1 \- forward sense, \-1 \- reverse sense .RE .PP \fB\-minscore\fR \fIfloat\fR .RS 4 Minimum score of feature to display (see also maxscore) Default value: 0\&.0 .RE .PP \fB\-maxscore\fR \fIfloat\fR .RS 4 Maximum score of feature to display\&. If both minscore and maxscore are zero (the default), then any score is ignored Default value: 0\&.0 .RE .PP \fB\-tagmatch\fR \fIstring\fR .RS 4 Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \*(AqCDS\*(Aq type of feature may have the tags \*(Aq/codon\*(Aq, \*(Aq/codon_start\*(Aq, \*(Aq/db_xref\*(Aq, \*(Aq/EC_number\*(Aq, \*(Aq/evidence\*(Aq, \*(Aq/exception\*(Aq, \*(Aq/function\*(Aq, \*(Aq/gene\*(Aq, \*(Aq/label\*(Aq, \*(Aq/map\*(Aq, \*(Aq/note\*(Aq, \*(Aq/number\*(Aq, \*(Aq/partial\*(Aq, \*(Aq/product\*(Aq, \*(Aq/protein_id\*(Aq, \*(Aq/pseudo\*(Aq, \*(Aq/standard_name\*(Aq, \*(Aq/translation\*(Aq, \*(Aq/transl_except\*(Aq, \*(Aq/transl_table\*(Aq, or \*(Aq/usedin\*(Aq\&. Some of these tags also have values, for example \*(Aq/gene\*(Aq can have the value of the gene name\&. By default any feature tag in the feature table is shown\&. You can set this to match any feature tag you wish to show\&. The tag may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one tag, separate their names with the character \*(Aq|\*(Aq, eg: gene | label Default value: * .RE .PP \fB\-valuematch\fR \fIstring\fR .RS 4 Tag values are the values associated with a feature tag\&. Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \*(AqCDS\*(Aq type of feature may have the tags \*(Aq/codon\*(Aq, \*(Aq/codon_start\*(Aq, \*(Aq/db_xref\*(Aq, \*(Aq/EC_number\*(Aq, \*(Aq/evidence\*(Aq, \*(Aq/exception\*(Aq, \*(Aq/function\*(Aq, \*(Aq/gene\*(Aq, \*(Aq/label\*(Aq, \*(Aq/map\*(Aq, \*(Aq/note\*(Aq, \*(Aq/number\*(Aq, \*(Aq/partial\*(Aq, \*(Aq/product\*(Aq, \*(Aq/protein_id\*(Aq, \*(Aq/pseudo\*(Aq, \*(Aq/standard_name\*(Aq, \*(Aq/translation\*(Aq, \*(Aq/transl_except\*(Aq, \*(Aq/transl_table\*(Aq, or \*(Aq/usedin\*(Aq\&. Only some of these tags can have values, for example \*(Aq/gene\*(Aq can have the value of the gene name\&. By default any feature tag value in the feature table is shown\&. You can set this to match any feature tag value you wish to show\&. The tag value may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one tag value, separate their names with the character \*(Aq|\*(Aq, eg: pax* | 10 Default value: * .RE .PP \fB\-stricttags\fR \fIboolean\fR .RS 4 By default if any tag/value pair in a feature matches the specified tag and value, then all the tags/value pairs of that feature will be displayed\&. If this is set to be true, then only those tag/value pairs in a feature that match the specified tag and value will be displayed\&. Default value: N .RE .SS "Advanced section" .SS "Restriction map options" .PP \fB\-flatreformat\fR \fIboolean\fR .RS 4 This changes the output format to one where the recognition site is indicated by a row of \*(Aq===\*(Aq characters and the cut site is pointed to by a \*(Aq>\*(Aq character in the forward sense, or a \*(Aq<\*(Aq in the reverse sense strand\&. Default value: N .RE .PP \fB\-mincuts\fR \fIinteger\fR .RS 4 This sets the minimum number of cuts for any restriction enzyme that will be considered\&. Any enzymes that cut fewer times than this will be ignored\&. Default value: 1 .RE .PP \fB\-maxcuts\fR \fIinteger\fR .RS 4 This sets the maximum number of cuts for any restriction enzyme that will be considered\&. Any enzymes that cut more times than this will be ignored\&. Default value: 2000000000 .RE .PP \fB\-sitelen\fR \fIinteger\fR .RS 4 This sets the minimum length of the restriction enzyme recognition site\&. Any enzymes with sites shorter than this will be ignored\&. Default value: 4 .RE .PP \fB\-single\fR \fIboolean\fR .RS 4 If this is set then this forces the values of the mincuts and maxcuts qualifiers to both be 1\&. Any other value you may have set them to will be ignored\&. Default value: N .RE .PP \fB\-blunt\fR \fIboolean\fR .RS 4 This allows those enzymes which cut at the same position on the forward and reverse strands to be considered\&. Default value: Y .RE .PP \fB\-sticky\fR \fIboolean\fR .RS 4 This allows those enzymes which cut at different positions on the forward and reverse strands, leaving an overhang, to be considered\&. Default value: Y .RE .PP \fB\-ambiguity\fR \fIboolean\fR .RS 4 This allows those enzymes which have one or more \*(AqN\*(Aq ambiguity codes in their pattern to be considered Default value: Y .RE .PP \fB\-plasmid\fR \fIboolean\fR .RS 4 If this is set then this allows searches for restriction enzyme recognition site and cut positions that span the end of the sequence to be considered\&. Default value: N .RE .PP \fB\-methylation\fR \fIboolean\fR .RS 4 If this is set then RE recognition sites will not match methylated bases\&. Default value: N .RE .PP \fB\-commercial\fR \fIboolean\fR .RS 4 If this is set, then only those enzymes with a commercial supplier will be searched for\&. This qualifier is ignored if you have specified an explicit list of enzymes to search for, rather than searching through \*(Aqall\*(Aq the enzymes in the REBASE database\&. It is assumed that, if you are asking for an explicit enzyme, then you probably know where to get it from and so all enzymes names that you have asked to be searched for, and which cut, will be reported whether or not they have a commercial supplier\&. Default value: Y .RE .PP \fB\-limit\fR \fIboolean\fR .RS 4 This limits the reporting of enzymes to just one enzyme from each group of isoschizomers\&. The enzyme chosen to represent an isoschizomer group is the prototype indicated in the data file \*(Aqembossre\&.equ\*(Aq, which is created by the program \*(Aqrebaseextract\*(Aq\&. If you prefer different prototypes to be used, make a copy of embossre\&.equ in your home directory and edit it\&. If this value is set to be false then all of the input enzymes will be reported\&. You might like to set this to false if you are supplying an explicit set of enzymes rather than searching \*(Aqall\*(Aq of them\&. Default value: Y .RE .PP \fB\-orfminsize\fR \fIinteger\fR .RS 4 This sets the minimum size of Open Reading Frames (ORFs) to display in the translations\&. All other translation regions are masked by changing the amino acids to \*(Aq\-\*(Aq characters\&. .RE .PP \fB\-threeletter\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-number\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-width\fR \fIinteger\fR .RS 4 Default value: 60 .RE .PP \fB\-length\fR \fIinteger\fR .RS 4 .RE .PP \fB\-margin\fR \fIinteger\fR .RS 4 Default value: 10 .RE .PP \fB\-name\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to display the ID name of the sequence Default value: Y .RE .PP \fB\-description\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to display the description of the sequence Default value: Y .RE .PP \fB\-offset\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-html\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP showseq is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/edamhasinput.1e0000644000000000000000000000677712214054043013706 0ustar '\" t .\" Title: EDAMHASINPUT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "EDAMHASINPUT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" edamhasinput \- Find EDAM ontology terms by has_input relation .SH "SYNOPSIS" .HP \w'\fBedamhasinput\fR\ 'u \fBedamhasinput\fR \fB\-identifier\ \fR\fB\fIstring\fR\fR [\fB\-namespace\ \fR\fB\fIlist\fR\fR] \fB\-sensitive\ \fR\fB\fIboolean\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-edamhasinput\ \fR\fB\fIoutobo\fR\fR .HP \w'\fBedamhasinput\fR\ 'u \fBedamhasinput\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBedamhasinput\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Data retrieval:Ontology data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-identifier\fR \fIstring\fR .RS 4 .RE .SS "Additional section" .PP \fB\-namespace\fR \fIlist\fR .RS 4 By default all terms are returned\&. Searches can be limited to one or a few namespaces\&. Default value: * .RE .SS "Advanced section" .PP \fB\-sensitive\fR \fIboolean\fR .RS 4 By default, the query keywords are matched against the EDAM term names (and synonyms) only\&. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches\&. Default value: N .RE .PP \fB\-subclasses\fR \fIboolean\fR .RS 4 Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: N .RE .PP \fB\-obsolete\fR \fIboolean\fR .RS 4 The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N .RE .SS "Output section" .PP \fB\-edamhasinput\fR \fIoutobo\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP edamhasinput is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/dbget.1e0000644000000000000000000001001012214054043012260 0ustar '\" t .\" Title: DBGET .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DBGET" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" dbget \- Retrieve database entries for a named database, data type and data identifier .SH "SYNOPSIS" .HP \w'\fBdbget\fR\ 'u \fBdbget\fR \fB\-database\ \fR\fB\fIstring\fR\fR \fB\-datatype\ \fR\fB\fIstring\fR\fR \fB\-identifier\ \fR\fB\fIstring\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] \fB\-outdir\ \fR\fB\fIoutdir\fR\fR .HP \w'\fBdbget\fR\ 'u \fBdbget\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdbget\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Misc" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-database\fR \fIstring\fR .RS 4 This is the name of a database from the catalogue of public databases in the EMBOSS data file DRCAT\&.dat\&. If you are unsure of the available databases use dbfind\&. If you have a database name but are not sure its valid, use isdbname\&. .RE .PP \fB\-datatype\fR \fIstring\fR .RS 4 This is the name of a retrievable datatype from the catalogue of public databases in the EMBOSS data file DRCAT\&.dat\&. The names are terms from the \*(Aqdata\*(Aq branch of the EDAM ontology, http://edamontology\&.sourceforge\&.net/\&. If you are unsure of the available retrievable datatypes for a given database, use dbtellquery\&. If you have a datatype name but are not sure its valid, use isdbdata\&. .RE .PP \fB\-identifier\fR \fIstring\fR .RS 4 This is a data identifier (e\&.g\&. a sequence accession number) that is used to specify the data (of type \*(Aqdatatype\*(Aq) to retrieve\&. If you\*(Aqre unsure of the data identifier(s) that are used for a given query (database/datatype) use dbtellquery\&. The types of data identifier are listed under the \*(AqData identifier\*(Aq branch of the EDAM ontology (http://edamontology\&.sourceforge\&.net/)\&. For example values, see the catalogue of public databases in the EMBOSS data file DRCAT\&.dat\&. If you have a data identifier but are unsure of its type, use idtell\&. .RE .SS "Required section" .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .PP \fB\-outdir\fR \fIoutdir\fR .RS 4 Default value: \&. .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP dbget is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/acdvalid.1e0000644000000000000000000000441512214054043012756 0ustar '\" t .\" Title: ACDVALID .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ACDVALID" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" acdvalid \- Validate an application ACD file .SH "SYNOPSIS" .HP \w'\fBacdvalid\fR\ 'u \fBacdvalid\fR .HP \w'\fBacdvalid\fR\ 'u \fBacdvalid\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBacdvalid\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Acd,Data retrieval:Tool data" command group(s)\&. .SH "OPTIONS" .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP acdvalid is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/wossinput.1e0000644000000000000000000001603612214054043013264 0ustar '\" t .\" Title: WOSSINPUT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "WOSSINPUT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" wossinput \- Finds programs by EDAM input data .SH "SYNOPSIS" .HP \w'\fBwossinput\fR\ 'u \fBwossinput\fR \fB\-identifier\ \fR\fB\fIstring\fR\fR [\fB\-explode\ \fR\fB\fIboolean\fR\fR] [\fB\-showkeywords\ \fR\fB\fIboolean\fR\fR] \fB\-sensitive\ \fR\fB\fIboolean\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-emboss\ \fR\fB\fIboolean\fR\fR \fB\-embassy\ \fR\fB\fIboolean\fR\fR \fB\-showembassy\ \fR\fB\fIstring\fR\fR \fB\-colon\ \fR\fB\fIboolean\fR\fR \fB\-gui\ \fR\fB\fIboolean\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fItoggle\fR\fR] [\fB\-groups\ \fR\fB\fIboolean\fR\fR] [\fB\-alphabetic\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBwossinput\fR\ 'u \fBwossinput\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBwossinput\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Documentation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-identifier\fR \fIstring\fR .RS 4 .RE .SS "Additional section" .PP \fB\-explode\fR \fIboolean\fR .RS 4 The groups that EMBOSS applications belong to have two forms, exploded and not exploded\&. The exploded group names are more numerous and often vaguely phrased than the non\-exploded ones\&. The exploded names are formed from definitions of the group names that start like NAME1:NAME2 and which are then expanded into many combinations of the names as: \*(AqNAME1\*(Aq, \*(AqNAME2\*(Aq, \*(AqNAME1 NAME2\*(Aq, NAME2 NAME1\*(Aq\&. The non\-expanded names are simply like: \*(AqNAME1 NAME2\*(Aq\&. Default value: N .RE .PP \fB\-showkeywords\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Advanced section" .PP \fB\-sensitive\fR \fIboolean\fR .RS 4 By default, the query keywords are matched against the EDAM term names (and synonyms) only\&. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches\&. Default value: N .RE .PP \fB\-subclasses\fR \fIboolean\fR .RS 4 Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: Y .RE .PP \fB\-obsolete\fR \fIboolean\fR .RS 4 The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N .RE .PP \fB\-emboss\fR \fIboolean\fR .RS 4 If you use this option then EMBOSS program documentation will be searched\&. If this option is set to be false, then only the EMBASSY programs will be searched (if the \-embassy option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y .RE .PP \fB\-embassy\fR \fIboolean\fR .RS 4 If you use this option then EMBASSY program documentation will be searched\&. If this option is set to be false, then only the EMBOSS programs will be searched (if the \-emboss option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y .RE .PP \fB\-showembassy\fR \fIstring\fR .RS 4 If you use this option then this EMBASSY package program documentation will be searched\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme .RE .PP \fB\-colon\fR \fIboolean\fR .RS 4 The groups that EMBOSS applications belong to up to two levels, for example the primary group \*(AqALIGNMENT\*(Aq has several sub\-groups, or second\-level groups, e\&.g\&.: CONSENSUS, DIFFERENCES, DOT PLOTS, GLOBAL, LOCAL, MULTIPLE\&. To aid programs that parse the output of wossname that require the names of these subgroups, a colon \*(Aq:\*(Aq will be placed between the first and second level of the group name if this option is true\&. Note: This does not apply if the group names have been exploded with the \*(Aqexplode\*(Aq option\&. Default value: N .RE .PP \fB\-gui\fR \fIboolean\fR .RS 4 This option is intended to help those who are designing Graphical User Interfaces to the EMBOSS applications\&. Some EMBOSS programs are inappropriate for running in a GUI, these include other menu programs and interactive editors\&. This option allows you to only report those programs that can be run from a GUI Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .SS "Html section" .PP \fB\-html\fR \fItoggle\fR .RS 4 If you are sending the output to a file, this will format it for displaying as a table in a WWW document\&. Default value: N .RE .PP \fB\-groups\fR \fIboolean\fR .RS 4 If you use this option, then only the group names will be output to the file Default value: N .RE .PP \fB\-alphabetic\fR \fIboolean\fR .RS 4 If you use this option, then you will get a single list of the program names and descriptions instead of the programs being listed in their functional groups\&. Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP wossinput is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/dbshowquery.1e0000644000000000000000000001025612214054043013563 0ustar '\" t .\" Title: DBSHOWQUERY .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DBSHOWQUERY" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" dbshowquery \- Show possible database queries that use a given data identifier .SH "SYNOPSIS" .HP \w'\fBdbshowquery\fR\ 'u \fBdbshowquery\fR \fB\-identifier\ \fR\fB\fIstring\fR\fR \fB\-database\ \fR\fB\fIstring\fR\fR \fB\-datatype\ \fR\fB\fIstring\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBdbshowquery\fR\ 'u \fBdbshowquery\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdbshowquery\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Information" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-identifier\fR \fIstring\fR .RS 4 This is a data identifier (e\&.g\&. a sequence accession number) that is used to specify the data (of type \*(Aqdatatype\*(Aq) to retrieve\&. If you\*(Aqre unsure of the data identifier(s) that are used for a given query (database/datatype) use dbtellquery\&. The types of data identifier are listed under the \*(AqData identifier\*(Aq branch of the EDAM ontology (http://edamontology\&.sourceforge\&.net/)\&. For example values, see the catalogue of public databases in the EMBOSS data file DRCAT\&.dat\&. If you have a data identifier but are unsure of its type, use idtell\&. .RE .SS "Required section" .SS "Additional section" .SS "Advanced section" .PP \fB\-database\fR \fIstring\fR .RS 4 This is the name of a database from the catalogue of public databases in the EMBOSS data file DRCAT\&.dat\&. If you are unsure of the available databases use drfind\&. If you have a database name but are not sure its valid, use isdbname\&. .RE .PP \fB\-datatype\fR \fIstring\fR .RS 4 This is the name of a retrievable datatype from the catalogue of public databases in the EMBOSS data file DRCAT\&.dat\&. The names are terms from the \*(Aqdata\*(Aq branch of the EDAM ontology, http://edamontology\&.sourceforge\&.net/\&. If you are unsure of the available retrievable datatypes for a given database, use dbtellquery\&. If you have a datatype name but are not sure its valid, use isdbdata\&. .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .SS "Html section" .PP \fB\-html\fR \fIboolean\fR .RS 4 If you are sending the output to a file, this will format it for displaying as a table in a WWW document\&. Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP dbshowquery is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/cacheensembl.1e0000644000000000000000000000522612214054043013621 0ustar '\" t .\" Title: CACHEENSEMBL .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "CACHEENSEMBL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" cacheensembl \- Generates server cache file for an Ensembl server .SH "SYNOPSIS" .HP \w'\fBcacheensembl\fR\ 'u \fBcacheensembl\fR \fB\-servername\ \fR\fB\fIstring\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] \fB\-cachefile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBcacheensembl\fR\ 'u \fBcacheensembl\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBcacheensembl\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data resources" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-servername\fR \fIstring\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .PP \fB\-cachefile\fR \fIoutfile\fR .RS 4 Default value: server\&.$(servername) .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP cacheensembl is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/silent.1e0000644000000000000000000000557012214054043012510 0ustar '\" t .\" Title: SILENT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SILENT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" silent \- Find restriction sites to insert (mutate) with no translation change .SH "SYNOPSIS" .HP \w'\fBsilent\fR\ 'u \fBsilent\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-enzymes\ \fR\fB\fIstring\fR\fR \fB\-sshow\ \fR\fB\fIboolean\fR\fR \fB\-tshow\ \fR\fB\fIboolean\fR\fR \fB\-allmut\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR .HP \w'\fBsilent\fR\ 'u \fBsilent\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBsilent\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Restriction" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .SS "Required section" .PP \fB\-enzymes\fR \fIstring\fR .RS 4 Default value: all .RE .SS "Output section" .PP \fB\-sshow\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-tshow\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-allmut\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-outfile\fR \fIreport\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP silent is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/entrailswiki.1e0000644000000000000000000000500312214054043013706 0ustar '\" t .\" Title: ENTRAILSWIKI .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ENTRAILSWIKI" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" entrailswiki \- Reports the internal structures in wikitext .SH "SYNOPSIS" .HP \w'\fBentrailswiki\fR\ 'u \fBentrailswiki\fR \fB\-tables\ \fR\fB\fIlist\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBentrailswiki\fR\ 'u \fBentrailswiki\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBentrailswiki\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Misc" command group(s)\&. .SH "OPTIONS" .SS "required section" .PP \fB\-tables\fR \fIlist\fR .RS 4 Default value: all .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP entrailswiki is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/aaindexextract.1e0000644000000000000000000000465412214054043014220 0ustar '\" t .\" Title: AAINDEXEXTRACT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "AAINDEXEXTRACT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" aaindexextract \- Extract amino acid property data from AAINDEX .SH "SYNOPSIS" .HP \w'\fBaaindexextract\fR\ 'u \fBaaindexextract\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR .HP \w'\fBaaindexextract\fR\ 'u \fBaaindexextract\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBaaindexextract\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP aaindexextract is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/dastest.1e0000644000000000000000000000716412214054043012662 0ustar '\" t .\" Title: DASTEST .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DASTEST" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" dastest \- Return DAS sources from a DAS server or from the DAS registry .SH "SYNOPSIS" .HP \w'\fBdastest\fR\ 'u \fBdastest\fR [\fB\-sequencesourcesonly\ \fR\fB\fIboolean\fR\fR] [\fB\-entrypoints\ \fR\fB\fIboolean\fR\fR] [\fB\-showtestqueries\ \fR\fB\fIboolean\fR\fR] [\fB\-runtestqueries\ \fR\fB\fIboolean\fR\fR] \fB\-host\ \fR\fB\fIstring\fR\fR \fB\-path\ \fR\fB\fIstring\fR\fR \fB\-port\ \fR\fB\fIinteger\fR\fR \fB\-servername\ \fR\fB\fIstring\fR\fR \fB\-maxtests\ \fR\fB\fIinteger\fR\fR \fB\-maxfeatures\ \fR\fB\fIinteger\fR\fR \fB\-maxsegments\ \fR\fB\fIinteger\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] .HP \w'\fBdastest\fR\ 'u \fBdastest\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdastest\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Display,Information" command group(s)\&. .SH "OPTIONS" .SS "Input section" .SS "Additional section" .PP \fB\-sequencesourcesonly\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-entrypoints\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-showtestqueries\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-runtestqueries\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Advanced section" .PP \fB\-host\fR \fIstring\fR .RS 4 Default value: www\&.dasregistry\&.org .RE .PP \fB\-path\fR \fIstring\fR .RS 4 Default value: /das .RE .PP \fB\-port\fR \fIinteger\fR .RS 4 Default value: 80 .RE .PP \fB\-servername\fR \fIstring\fR .RS 4 Default value: das .RE .PP \fB\-maxtests\fR \fIinteger\fR .RS 4 Default value: 80 .RE .PP \fB\-maxfeatures\fR \fIinteger\fR .RS 4 Default value: 80 .RE .PP \fB\-maxsegments\fR \fIinteger\fR .RS 4 Default value: 5 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP dastest is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/water.1e0000644000000000000000000001010612214054043012323 0ustar '\" t .\" Title: WATER .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "WATER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" water \- Smith\-Waterman local alignment of sequences .SH "SYNOPSIS" .HP \w'\fBwater\fR\ 'u \fBwater\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIseqall\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] \fB\-gapopen\ \fR\fB\fIfloat\fR\fR \fB\-gapextend\ \fR\fB\fIfloat\fR\fR \fB\-brief\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIalign\fR\fR .HP \w'\fBwater\fR\ 'u \fBwater\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBwater\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Local" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-asequence\fR \fIsequence\fR .RS 4 .RE .PP \fB\-bsequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-datafile\fR \fImatrixf\fR .RS 4 This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&. .RE .SS "Required section" .PP \fB\-gapopen\fR \fIfloat\fR .RS 4 The gap open penalty is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: @($(acdprotein)? 10\&.0 : 10\&.0) .RE .PP \fB\-gapextend\fR \fIfloat\fR .RS 4 The gap extension penalty is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps\&. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring\&. Default value: @($(acdprotein)? 0\&.5 : 0\&.5) .RE .SS "Output section" .PP \fB\-brief\fR \fIboolean\fR .RS 4 Brief identity and similarity Default value: Y .RE .PP \fB\-outfile\fR \fIalign\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP water is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/wossname.1e0000644000000000000000000001535712214054043013052 0ustar '\" t .\" Title: WOSSNAME .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "WOSSNAME" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" wossname \- Finds programs by keywords in their short description .SH "SYNOPSIS" .HP \w'\fBwossname\fR\ 'u \fBwossname\fR \fB\-search\ \fR\fB\fIstring\fR\fR [\fB\-explode\ \fR\fB\fIboolean\fR\fR] [\fB\-allmatch\ \fR\fB\fIboolean\fR\fR] [\fB\-showkeywords\ \fR\fB\fIboolean\fR\fR] \fB\-emboss\ \fR\fB\fIboolean\fR\fR \fB\-embassy\ \fR\fB\fIboolean\fR\fR \fB\-showembassy\ \fR\fB\fIstring\fR\fR \fB\-colon\ \fR\fB\fIboolean\fR\fR \fB\-gui\ \fR\fB\fIboolean\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fItoggle\fR\fR] [\fB\-groups\ \fR\fB\fIboolean\fR\fR] [\fB\-alphabetic\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBwossname\fR\ 'u \fBwossname\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBwossname\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Documentation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-search\fR \fIstring\fR .RS 4 Enter a word or words here and a case\-independent search for it will be made in the one\-line documentation, group names and keywords of all of the EMBOSS programs\&. If no keyword is specified, all programs will be listed\&. .RE .SS "Additional section" .PP \fB\-explode\fR \fIboolean\fR .RS 4 The groups that EMBOSS applications belong to have two forms, exploded and not exploded\&. The exploded group names are more numerous and often vaguely phrased than the non\-exploded ones\&. The exploded names are formed from definitions of the group names that start like NAME1:NAME2 and which are then expanded into many combinations of the names as: \*(AqNAME1\*(Aq, \*(AqNAME2\*(Aq, \*(AqNAME1 NAME2\*(Aq, NAME2 NAME1\*(Aq\&. The non\-expanded names are simply like: \*(AqNAME1 NAME2\*(Aq\&. Default value: N .RE .PP \fB\-allmatch\fR \fIboolean\fR .RS 4 By default, all words in the search string must match\&. This option searches for a match to any word in a list of possibilities Default value: Y .RE .PP \fB\-showkeywords\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Advanced section" .PP \fB\-emboss\fR \fIboolean\fR .RS 4 If you use this option then EMBOSS program documentation will be searched\&. If this option is set to be false, then only the EMBASSY programs will be searched (if the \-embassy option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y .RE .PP \fB\-embassy\fR \fIboolean\fR .RS 4 If you use this option then EMBASSY program documentation will be searched\&. If this option is set to be false, then only the EMBOSS programs will be searched (if the \-emboss option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y .RE .PP \fB\-showembassy\fR \fIstring\fR .RS 4 If you use this option then this EMBASSY package program documentation will be searched\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme .RE .PP \fB\-colon\fR \fIboolean\fR .RS 4 The groups that EMBOSS applications belong to up to two levels, for example the primary group \*(AqALIGNMENT\*(Aq has several sub\-groups, or second\-level groups, e\&.g\&.: CONSENSUS, DIFFERENCES, DOT PLOTS, GLOBAL, LOCAL, MULTIPLE\&. To aid programs that parse the output of wossname that require the names of these subgroups, a colon \*(Aq:\*(Aq will be placed between the first and second level of the group name if this option is true\&. Note: This does not apply if the group names have been exploded with the \*(Aqexplode\*(Aq option\&. Default value: N .RE .PP \fB\-gui\fR \fIboolean\fR .RS 4 This option is intended to help those who are designing Graphical User Interfaces to the EMBOSS applications\&. Some EMBOSS programs are inappropriate for running in a GUI, these include other menu programs and interactive editors\&. This option allows you to only report those programs that can be run from a GUI Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .SS "Html section" .PP \fB\-html\fR \fItoggle\fR .RS 4 If you are sending the output to a file, this will format it for displaying as a table in a WWW document\&. Default value: N .RE .PP \fB\-groups\fR \fIboolean\fR .RS 4 If you use this option, then only the group names will be output to the file Default value: N .RE .PP \fB\-alphabetic\fR \fIboolean\fR .RS 4 If you use this option, then you will get a single list of the program names and descriptions instead of the programs being listed in their functional groups\&. Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP wossname is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/acdtrace.1e0000644000000000000000000000461412214054043012756 0ustar '\" t .\" Title: ACDTRACE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ACDTRACE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" acdtrace \- Trace processing of an application ACD file (for testing) .SH "SYNOPSIS" .HP \w'\fBacdtrace\fR\ 'u \fBacdtrace\fR \fB\-program\ \fR\fB\fIstring\fR\fR .HP \w'\fBacdtrace\fR\ 'u \fBacdtrace\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBacdtrace\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Acd,Data retrieval:Tool data" command group(s)\&. .SH "OPTIONS" .SS "Required section" .PP \fB\-program\fR \fIstring\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP acdtrace is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/shuffleseq.1e0000644000000000000000000000517512214054043013360 0ustar '\" t .\" Title: SHUFFLESEQ .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SHUFFLESEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" shuffleseq \- Shuffles a set of sequences maintaining composition .SH "SYNOPSIS" .HP \w'\fBshuffleseq\fR\ 'u \fBshuffleseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-shuffle\ \fR\fB\fIinteger\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBshuffleseq\fR\ 'u \fBshuffleseq\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBshuffleseq\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Mutation,Protein:Mutation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Advanced section" .PP \fB\-shuffle\fR \fIinteger\fR .RS 4 Default value: 1 .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP shuffleseq is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/treetypedisplay.1e0000644000000000000000000000460212214054043014434 0ustar '\" t .\" Title: TREETYPEDISPLAY .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "TREETYPEDISPLAY" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" treetypedisplay \- Test of graphics .SH "SYNOPSIS" .HP \w'\fBtreetypedisplay\fR\ 'u \fBtreetypedisplay\fR \fB\-graph\ \fR\fB\fIgraph\fR\fR .HP \w'\fBtreetypedisplay\fR\ 'u \fBtreetypedisplay\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBtreetypedisplay\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Test" command group(s)\&. .SH "OPTIONS" .SS "Output section" .PP \fB\-graph\fR \fIgraph\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP treetypedisplay is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/dbtellquery.1e0000644000000000000000000000652112214054043013543 0ustar '\" t .\" Title: DBTELLQUERY .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DBTELLQUERY" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" dbtellquery \- Show possible queries of a database .SH "SYNOPSIS" .HP \w'\fBdbtellquery\fR\ 'u \fBdbtellquery\fR \fB\-database\ \fR\fB\fIstring\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBdbtellquery\fR\ 'u \fBdbtellquery\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdbtellquery\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Information" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-database\fR \fIstring\fR .RS 4 The unique identifier of the database\&. These are listed in the EMBOSS data file DRCAT\&.dat (field names in parenthesis) and can be the recommended or official unique identifier (\*(AqID\*(Aq), the alternative identifier (\*(AqIDalt\*(Aq), or the accession number (\*(AqAcc\*(Aq) of the database\&. Any of these are acceptable\&. Official database identifiers and accession numbers are taken from http://www\&.uniprot\&.org/docs/dbxref where available\&. You can use dbfind to find databases by keyword and return unique identifiers and other information\&. .RE .SS "Required section" .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .SS "Html section" .PP \fB\-html\fR \fIboolean\fR .RS 4 If you are sending the output to a file, this will format it for displaying as a table in a WWW document\&. Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP dbtellquery is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/martattributes.1e0000644000000000000000000000557512214054043014271 0ustar '\" t .\" Title: MARTATTRIBUTES .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "MARTATTRIBUTES" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" martattributes \- Return attributes from a mart dataset from a mart host .SH "SYNOPSIS" .HP \w'\fBmartattributes\fR\ 'u \fBmartattributes\fR \fB\-dataset\ \fR\fB\fIstring\fR\fR \fB\-host\ \fR\fB\fIstring\fR\fR \fB\-path\ \fR\fB\fIstring\fR\fR \fB\-port\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBmartattributes\fR\ 'u \fBmartattributes\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBmartattributes\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-dataset\fR \fIstring\fR .RS 4 Default value: oanatinus_gene_ensembl .RE .SS "Advanced section" .PP \fB\-host\fR \fIstring\fR .RS 4 Default value: www\&.biomart\&.org .RE .PP \fB\-path\fR \fIstring\fR .RS 4 Default value: /biomart/martservice .RE .PP \fB\-port\fR \fIinteger\fR .RS 4 Default value: 80 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP martattributes is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/showpep.1e0000644000000000000000000002051112214054043012667 0ustar '\" t .\" Title: SHOWPEP .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SHOWPEP" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" showpep \- Displays protein sequences with features in pretty format .SH "SYNOPSIS" .HP \w'\fBshowpep\fR\ 'u \fBshowpep\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-format\ \fR\fB\fIlist\fR\fR \fB\-things\ \fR\fB\fIlist\fR\fR [\fB\-uppercase\ \fR\fB\fIrange\fR\fR] [\fB\-highlight\ \fR\fB\fIrange\fR\fR] [\fB\-annotation\ \fR\fB\fIrange\fR\fR] [\fB\-sourcematch\ \fR\fB\fIstring\fR\fR] [\fB\-typematch\ \fR\fB\fIstring\fR\fR] [\fB\-minscore\ \fR\fB\fIfloat\fR\fR] [\fB\-maxscore\ \fR\fB\fIfloat\fR\fR] [\fB\-tagmatch\ \fR\fB\fIstring\fR\fR] [\fB\-valuematch\ \fR\fB\fIstring\fR\fR] [\fB\-stricttags\ \fR\fB\fIboolean\fR\fR] \fB\-threeletter\ \fR\fB\fIboolean\fR\fR \fB\-number\ \fR\fB\fIboolean\fR\fR \fB\-width\ \fR\fB\fIinteger\fR\fR \fB\-length\ \fR\fB\fIinteger\fR\fR \fB\-margin\ \fR\fB\fIinteger\fR\fR \fB\-name\ \fR\fB\fIboolean\fR\fR \fB\-description\ \fR\fB\fIboolean\fR\fR \fB\-offset\ \fR\fB\fIinteger\fR\fR \fB\-html\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBshowpep\fR\ 'u \fBshowpep\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBshowpep\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Display" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Required section" .PP \fB\-format\fR \fIlist\fR .RS 4 Default value: 2 .RE .PP \fB\-things\fR \fIlist\fR .RS 4 Specify a list of one or more code characters in the order in which you wish things to be displayed one above the other down the page\&. For example if you wish to see things displayed in the order: sequence, ticks line, blank line; then you should enter \*(AqS,T,B\*(Aq\&. Default value: B,N,T,S,A,F .RE .SS "Additional section" .PP \fB\-uppercase\fR \fIrange\fR .RS 4 Regions to put in uppercase\&. If this is left blank, then the sequence case is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 24\-45, 56\-78 1:45, 67=99;765\&.\&.888 1,5,8,10,23,45,57,99 .RE .PP \fB\-highlight\fR \fIrange\fR .RS 4 Regions to colour if formatting for HTML\&. If this is left blank, then the sequence is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are followed by any valid HTML font colour\&. Examples of region specifications are: 24\-45 blue 56\-78 orange 1\-100 green 120\-156 red A file of ranges to colour (one range per line) can be specified as \*(Aq@filename\*(Aq\&. .RE .PP \fB\-annotation\fR \fIrange\fR .RS 4 Regions to annotate by marking\&. If this is left blank, then no annotation is added\&. A set of regions is specified by a set of pairs of positions followed by optional text\&. The positions are integers\&. They are followed by any text (but not digits when on the command\-line)\&. Examples of region specifications are: 24\-45 new domain 56\-78 match to Mouse 1\-100 First part 120\-156 oligo A file of ranges to annotate (one range per line) can be specified as \*(Aq@filename\*(Aq\&. .RE .SS "Feature display options" .PP \fB\-sourcematch\fR \fIstring\fR .RS 4 By default any feature source in the feature table is shown\&. You can set this to match any feature source you wish to show\&. The source name is usually either the name of the program that detected the feature or it is the feature table (eg: EMBL) that the feature came from\&. The source may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one source, separate their names with the character \*(Aq|\*(Aq, eg: gene* | embl Default value: * .RE .PP \fB\-typematch\fR \fIstring\fR .RS 4 By default any feature type in the feature table is shown\&. You can set this to match any feature type you wish to show\&. See http://www\&.ebi\&.ac\&.uk/embl/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www\&.expasy\&.org/sprot/userman\&.html for a list of the Swissprot feature types\&. The type may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one type, separate their names with the character \*(Aq|\*(Aq, eg: *UTR | intron Default value: * .RE .PP \fB\-minscore\fR \fIfloat\fR .RS 4 Minimum score of feature to display (see also maxscore) Default value: 0\&.0 .RE .PP \fB\-maxscore\fR \fIfloat\fR .RS 4 Maximum score of feature to display\&. If both minscore and maxscore are zero (the default), then any score is ignored Default value: 0\&.0 .RE .PP \fB\-tagmatch\fR \fIstring\fR .RS 4 Tags are the types of extra values that a feature may have\&. By default any feature tag in the feature table is shown\&. You can set this to match any feature tag you wish to show\&. The tag may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one tag, separate their names with the character \*(Aq|\*(Aq, eg: gene | label Default value: * .RE .PP \fB\-valuematch\fR \fIstring\fR .RS 4 Tag values are the values associated with a feature tag\&. Tags are the types of extra values that a feature may have\&. By default any feature tag value in the feature table is shown\&. You can set this to match any feature tag value you wish to show\&. The tag value may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one tag value, separate their names with the character \*(Aq|\*(Aq, eg: pax* | 10 Default value: * .RE .PP \fB\-stricttags\fR \fIboolean\fR .RS 4 By default if any tag/value pair in a feature matches the specified tag and value, then all the tags/value pairs of that feature will be displayed\&. If this is set to be true, then only those tag/value pairs in a feature that match the specified tag and value will be displayed\&. Default value: N .RE .SS "Advanced section" .PP \fB\-threeletter\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-number\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-width\fR \fIinteger\fR .RS 4 Default value: 60 .RE .PP \fB\-length\fR \fIinteger\fR .RS 4 .RE .PP \fB\-margin\fR \fIinteger\fR .RS 4 Default value: 10 .RE .PP \fB\-name\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to display the ID name of the sequence Default value: Y .RE .PP \fB\-description\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to display the description of the sequence Default value: Y .RE .PP \fB\-offset\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-html\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP showpep is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/findkm.1e0000644000000000000000000000520012214054043012450 0ustar '\" t .\" Title: FINDKM .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "FINDKM" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" findkm \- Calculate and plot enzyme reaction data .SH "SYNOPSIS" .HP \w'\fBfindkm\fR\ 'u \fBfindkm\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-plot\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-graphlb\ \fR\fB\fIxygraph\fR\fR .HP \w'\fBfindkm\fR\ 'u \fBfindkm\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfindkm\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Enzyme Kinetics" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .SS "Advanced section" .PP \fB\-plot\fR \fIboolean\fR .RS 4 Default value: Y .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-graphlb\fR \fIxygraph\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP findkm is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/featreport.1e0000644000000000000000000000505112214054043013357 0ustar '\" t .\" Title: FEATREPORT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "FEATREPORT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" featreport \- Reads and writes a feature table .SH "SYNOPSIS" .HP \w'\fBfeatreport\fR\ 'u \fBfeatreport\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-features\ \fR\fB\fIfeatures\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR .HP \w'\fBfeatreport\fR\ 'u \fBfeatreport\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfeatreport\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .PP \fB\-features\fR \fIfeatures\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIreport\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP featreport is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/ontogetroot.1e0000644000000000000000000000540212214054043013567 0ustar '\" t .\" Title: ONTOGETROOT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ONTOGETROOT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" ontogetroot \- Get ontology root terms by child identifier .SH "SYNOPSIS" .HP \w'\fBontogetroot\fR\ 'u \fBontogetroot\fR \fB\-oboterms\ \fR\fB\fIobo\fR\fR [\fB\-obsolete\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutobo\fR\fR .HP \w'\fBontogetroot\fR\ 'u \fBontogetroot\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBontogetroot\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology,Data retrieval:Ontology data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-oboterms\fR \fIobo\fR .RS 4 .RE .SS "Additional section" .PP \fB\-obsolete\fR \fIboolean\fR .RS 4 The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N .RE .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutobo\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP ontogetroot is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/corbatest.1e0000644000000000000000000000472412214054043013200 0ustar '\" t .\" Title: CORBATEST .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "CORBATEST" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" corbatest \- Test of EMBL corba retrieval .SH "SYNOPSIS" .HP \w'\fBcorbatest\fR\ 'u \fBcorbatest\fR \fB\-entry\ \fR\fB\fIstring\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBcorbatest\fR\ 'u \fBcorbatest\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBcorbatest\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Test" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-entry\fR \fIstring\fR .RS 4 Default value: hsfau .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP corbatest is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/rebaseextract.1e0000644000000000000000000000534712214054043014050 0ustar '\" t .\" Title: REBASEEXTRACT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "REBASEEXTRACT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" rebaseextract \- Process the REBASE database for use by restriction enzyme applications .SH "SYNOPSIS" .HP \w'\fBrebaseextract\fR\ 'u \fBrebaseextract\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-protofile\ \fR\fB\fIinfile\fR\fR [\fB\-equivalences\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBrebaseextract\fR\ 'u \fBrebaseextract\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBrebaseextract\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .PP \fB\-protofile\fR \fIinfile\fR .RS 4 .RE .PP \fB\-equivalences\fR \fIboolean\fR .RS 4 This option calculates an embossre\&.equ file using restriction enzyme prototypes in the withrefm file\&. Default value: Y .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP rebaseextract is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/sigcleave.1e0000644000000000000000000000560112214054043013147 0ustar '\" t .\" Title: SIGCLEAVE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SIGCLEAVE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" sigcleave \- Reports on signal cleavage sites in a protein sequence .SH "SYNOPSIS" .HP \w'\fBsigcleave\fR\ 'u \fBsigcleave\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-minweight\ \fR\fB\fIfloat\fR\fR [\fB\-prokaryote\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIreport\fR\fR .HP \w'\fBsigcleave\fR\ 'u \fBsigcleave\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBsigcleave\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Functional sites,Protein:Motifs" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Required section" .PP \fB\-minweight\fR \fIfloat\fR .RS 4 Minimum scoring weight value for the predicted cleavage site Default value: 3\&.5 .RE .SS "Additional section" .PP \fB\-prokaryote\fR \fIboolean\fR .RS 4 Specifies the sequence is prokaryotic and changes the default scoring data file name .RE .SS "Output section" .PP \fB\-outfile\fR \fIreport\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP sigcleave is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/splitsource.1e0000644000000000000000000000517712214054043013571 0ustar '\" t .\" Title: SPLITSOURCE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SPLITSOURCE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" splitsource \- Split sequence(s) into original source sequences .SH "SYNOPSIS" .HP \w'\fBsplitsource\fR\ 'u \fBsplitsource\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBsplitsource\fR\ 'u \fBsplitsource\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBsplitsource\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-feature\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP splitsource is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/whichdb.1e0000644000000000000000000000523512214054043012620 0ustar '\" t .\" Title: WHICHDB .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "WHICHDB" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" whichdb \- Search all sequence databases for an entry and retrieve it .SH "SYNOPSIS" .HP \w'\fBwhichdb\fR\ 'u \fBwhichdb\fR \fB\-entry\ \fR\fB\fIstring\fR\fR \fB\-get\ \fR\fB\fItoggle\fR\fR \fB\-showall\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBwhichdb\fR\ 'u \fBwhichdb\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBwhichdb\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval:Sequence data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-entry\fR \fIstring\fR .RS 4 .RE .SS "Output section" .PP \fB\-get\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-showall\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP whichdb is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/drget.1e0000644000000000000000000000476412214054043012323 0ustar '\" t .\" Title: DRGET .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DRGET" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" drget \- Get data resource entries .SH "SYNOPSIS" .HP \w'\fBdrget\fR\ 'u \fBdrget\fR \fB\-resources\ \fR\fB\fIresource\fR\fR \fB\-outfile\ \fR\fB\fIoutresource\fR\fR .HP \w'\fBdrget\fR\ 'u \fBdrget\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdrget\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval:Resource data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-resources\fR \fIresource\fR .RS 4 .RE .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutresource\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP drget is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/drtext.1e0000644000000000000000000000503412214054043012517 0ustar '\" t .\" Title: DRTEXT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DRTEXT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" drtext \- Get data resource entries complete text .SH "SYNOPSIS" .HP \w'\fBdrtext\fR\ 'u \fBdrtext\fR \fB\-resources\ \fR\fB\fIresource\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBdrtext\fR\ 'u \fBdrtext\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdrtext\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval:Resource data,Data retrieval:Text data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-resources\fR \fIresource\fR .RS 4 .RE .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP drtext is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/plotcon.1e0000644000000000000000000000607512214054043012671 0ustar '\" t .\" Title: PLOTCON .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PLOTCON" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" plotcon \- Plot conservation of a sequence alignment .SH "SYNOPSIS" .HP \w'\fBplotcon\fR\ 'u \fBplotcon\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR [\fB\-scorefile\ \fR\fB\fImatrix\fR\fR] \fB\-winsize\ \fR\fB\fIinteger\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR .HP \w'\fBplotcon\fR\ 'u \fBplotcon\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBplotcon\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Multiple" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequences\fR \fIseqset\fR .RS 4 File containing a sequence alignment .RE .PP \fB\-scorefile\fR \fImatrix\fR .RS 4 This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&. .RE .SS "Required section" .PP \fB\-winsize\fR \fIinteger\fR .RS 4 Number of columns to average alignment quality over\&. The larger this value is, the smoother the plot will be\&. Default value: 4 .RE .SS "Output section" .PP \fB\-graph\fR \fIxygraph\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP plotcon is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/stssearch.1e0000644000000000000000000000507012214054043013204 0ustar '\" t .\" Title: STSSEARCH .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "STSSEARCH" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" stssearch \- Search a DNA database for matches with a set of STS primers .SH "SYNOPSIS" .HP \w'\fBstssearch\fR\ 'u \fBstssearch\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBstssearch\fR\ 'u \fBstssearch\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBstssearch\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Primers" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-seqall\fR \fIseqall\fR .RS 4 .RE .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP stssearch is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/extractalign.1e0000644000000000000000000000570612214054043013700 0ustar '\" t .\" Title: EXTRACTALIGN .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "EXTRACTALIGN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" extractalign \- Extract regions from a sequence alignment .SH "SYNOPSIS" .HP \w'\fBextractalign\fR\ 'u \fBextractalign\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR \fB\-regions\ \fR\fB\fIrange\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBextractalign\fR\ 'u \fBextractalign\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBextractalign\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment,Data retrieval:Sequence data,Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqset\fR .RS 4 .RE .SS "Required section" .PP \fB\-regions\fR \fIrange\fR .RS 4 Regions to extract\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 24\-45, 56\-78 1:45, 67=99;765\&.\&.888 1,5,8,10,23,45,57,99 Default value: $(sequence\&.begin)\-$(sequence\&.end) .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP extractalign is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/pepinfo.1e0000644000000000000000000000625612214054043012654 0ustar '\" t .\" Title: PEPINFO .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PEPINFO" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" pepinfo \- Plot amino acid properties of a protein sequence in parallel\&. .SH "SYNOPSIS" .HP \w'\fBpepinfo\fR\ 'u \fBpepinfo\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-aaproperties\ \fR\fB\fIdatafile\fR\fR] [\fB\-aahydropathy\ \fR\fB\fIdatafile\fR\fR] [\fB\-hwindow\ \fR\fB\fIinteger\fR\fR] \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-generalplot\ \fR\fB\fIboolean\fR\fR \fB\-hydropathyplot\ \fR\fB\fIboolean\fR\fR .HP \w'\fBpepinfo\fR\ 'u \fBpepinfo\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBpepinfo\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Composition,Protein:Properties,Display" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .PP \fB\-aaproperties\fR \fIdatafile\fR .RS 4 Default value: Eaa_properties\&.dat .RE .PP \fB\-aahydropathy\fR \fIdatafile\fR .RS 4 Default value: Eaa_hydropathy\&.dat .RE .SS "Additional section" .PP \fB\-hwindow\fR \fIinteger\fR .RS 4 Default value: 9 .RE .SS "Output section" .PP \fB\-graph\fR \fIxygraph\fR .RS 4 .RE .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-generalplot\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-hydropathyplot\fR \fIboolean\fR .RS 4 Default value: Y .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP pepinfo is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/nthseqset.1e0000644000000000000000000000526212214054043013226 0ustar '\" t .\" Title: NTHSEQSET .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "NTHSEQSET" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" nthseqset \- Reads and writes (returns) one set of sequences from many .SH "SYNOPSIS" .HP \w'\fBnthseqset\fR\ 'u \fBnthseqset\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqsetall\fR\fR \fB\-number\ \fR\fB\fIinteger\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBnthseqset\fR\ 'u \fBnthseqset\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBnthseqset\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-feature\fR \fIboolean\fR .RS 4 .RE .PP \fB\-sequence\fR \fIseqsetall\fR .RS 4 .RE .SS "Required section" .PP \fB\-number\fR \fIinteger\fR .RS 4 Default value: 1 .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP nthseqset is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/banana.1e0000644000000000000000000000551712214054043012433 0ustar '\" t .\" Title: BANANA .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "BANANA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" banana \- Plot bending and curvature data for B\-DNA .SH "SYNOPSIS" .HP \w'\fBbanana\fR\ 'u \fBbanana\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-anglesfile\ \fR\fB\fIdatafile\fR\fR] \fB\-graph\ \fR\fB\fIgraph\fR\fR [\fB\-residuesperline\ \fR\fB\fIinteger\fR\fR] [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] .HP \w'\fBbanana\fR\ 'u \fBbanana\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBbanana\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Properties,Nucleic:Composition,Nucleic:2D structure" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .PP \fB\-anglesfile\fR \fIdatafile\fR .RS 4 Default value: Eangles_tri\&.dat .RE .SS "Output section" .PP \fB\-graph\fR \fIgraph\fR .RS 4 .RE .PP \fB\-residuesperline\fR \fIinteger\fR .RS 4 Default value: 50 .RE .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: banana\&.profile .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP banana is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/cutseq.1e0000644000000000000000000000553412214054043012516 0ustar '\" t .\" Title: CUTSEQ .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "CUTSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" cutseq \- Removes a section from a sequence .SH "SYNOPSIS" .HP \w'\fBcutseq\fR\ 'u \fBcutseq\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-from\ \fR\fB\fIinteger\fR\fR \fB\-to\ \fR\fB\fIinteger\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR .HP \w'\fBcutseq\fR\ 'u \fBcutseq\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBcutseq\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .SS "Required section" .PP \fB\-from\fR \fIinteger\fR .RS 4 This is the start position (inclusive) of the section of the sequence that you wish to remove\&. Default value: $(sequence\&.begin) .RE .PP \fB\-to\fR \fIinteger\fR .RS 4 This is the end position (inclusive) of the section of the sequence that you wish to remove\&. Default value: $(sequence\&.end) .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqout\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP cutseq is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/extractseq.1e0000644000000000000000000000647012214054043013375 0ustar '\" t .\" Title: EXTRACTSEQ .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "EXTRACTSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" extractseq \- Extract regions from a sequence .SH "SYNOPSIS" .HP \w'\fBextractseq\fR\ 'u \fBextractseq\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-regions\ \fR\fB\fIrange\fR\fR [\fB\-separate\ \fR\fB\fIboolean\fR\fR] \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBextractseq\fR\ 'u \fBextractseq\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBextractseq\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .SS "Required section" .PP \fB\-regions\fR \fIrange\fR .RS 4 Regions to extract\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 24\-45, 56\-78 1:45, 67=99;765\&.\&.888 1,5,8,10,23,45,57,99 Default value: $(sequence\&.begin)\-$(sequence\&.end) .RE .SS "Additional section" .PP \fB\-separate\fR \fIboolean\fR .RS 4 If this is set true then each specified region is written out as a separate sequence\&. The name of the sequence is created from the name of the original sequence with the start and end positions of the range appended with underscore characters between them, eg: XYZ region 2 to 34 is written as: XYZ_2_34 Default value: N .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP extractseq is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/seqretsplit.1e0000644000000000000000000000525512214054043013571 0ustar '\" t .\" Title: SEQRETSPLIT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SEQRETSPLIT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" seqretsplit \- Reads sequences and writes them to individual files .SH "SYNOPSIS" .HP \w'\fBseqretsplit\fR\ 'u \fBseqretsplit\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-firstonly\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBseqretsplit\fR\ 'u \fBseqretsplit\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBseqretsplit\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-feature\fR \fIboolean\fR .RS 4 .RE .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Advanced section" .PP \fB\-firstonly\fR \fIboolean\fR .RS 4 .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP seqretsplit is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/taxgetspecies.1e0000644000000000000000000000507312214054043014060 0ustar '\" t .\" Title: TAXGETSPECIES .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "TAXGETSPECIES" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" taxgetspecies \- Get all species under taxon(s) .SH "SYNOPSIS" .HP \w'\fBtaxgetspecies\fR\ 'u \fBtaxgetspecies\fR \fB\-taxons\ \fR\fB\fItaxon\fR\fR \fB\-outfile\ \fR\fB\fIouttaxon\fR\fR .HP \w'\fBtaxgetspecies\fR\ 'u \fBtaxgetspecies\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBtaxgetspecies\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:Taxonomy" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-taxons\fR \fItaxon\fR .RS 4 .RE .SS "Required section" .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIouttaxon\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP taxgetspecies is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/martfilters.1e0000644000000000000000000000553712214054043013551 0ustar '\" t .\" Title: MARTFILTERS .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "MARTFILTERS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" martfilters \- Return filters from a mart dataset from a mart host .SH "SYNOPSIS" .HP \w'\fBmartfilters\fR\ 'u \fBmartfilters\fR \fB\-dataset\ \fR\fB\fIstring\fR\fR \fB\-host\ \fR\fB\fIstring\fR\fR \fB\-path\ \fR\fB\fIstring\fR\fR \fB\-port\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBmartfilters\fR\ 'u \fBmartfilters\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBmartfilters\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-dataset\fR \fIstring\fR .RS 4 Default value: oanatinus_gene_ensembl .RE .SS "Advanced section" .PP \fB\-host\fR \fIstring\fR .RS 4 Default value: www\&.biomart\&.org .RE .PP \fB\-path\fR \fIstring\fR .RS 4 Default value: /biomart/martservice .RE .PP \fB\-port\fR \fIinteger\fR .RS 4 Default value: 80 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP martfilters is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/emma.1e0000644000000000000000000003024112214054043012122 0ustar '\" t .\" Title: EMMA .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "EMMA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" emma \- Multiple sequence alignment (ClustalW wrapper) .SH "SYNOPSIS" .HP \w'\fBemma\fR\ 'u \fBemma\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-onlydend\ \fR\fB\fItoggle\fR\fR] \fB\-dend\ \fR\fB\fItoggle\fR\fR \fB\-dendfile\ \fR\fB\fIinfile\fR\fR [\fB\-slow\ \fR\fB\fItoggle\fR\fR] \fB\-pwmatrix\ \fR\fB\fIlist\fR\fR \fB\-pwdnamatrix\ \fR\fB\fIlist\fR\fR \fB\-usermatrix\ \fR\fB\fIvariable\fR\fR \fB\-pairwisedatafile\ \fR\fB\fIinfile\fR\fR \fB\-matrix\ \fR\fB\fIlist\fR\fR \fB\-usermamatrix\ \fR\fB\fIvariable\fR\fR \fB\-dnamatrix\ \fR\fB\fIlist\fR\fR \fB\-umamatrix\ \fR\fB\fIvariable\fR\fR \fB\-mamatrixfile\ \fR\fB\fIinfile\fR\fR \fB\-pwgapopen\ \fR\fB\fIfloat\fR\fR \fB\-pwgapextend\ \fR\fB\fIfloat\fR\fR \fB\-ktup\ \fR\fB\fIinteger\fR\fR \fB\-gapw\ \fR\fB\fIinteger\fR\fR \fB\-topdiags\ \fR\fB\fIinteger\fR\fR \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-nopercent\ \fR\fB\fIboolean\fR\fR [\fB\-gapopen\ \fR\fB\fIfloat\fR\fR] [\fB\-gapextend\ \fR\fB\fIfloat\fR\fR] [\fB\-endgaps\ \fR\fB\fIboolean\fR\fR] [\fB\-gapdist\ \fR\fB\fIinteger\fR\fR] \fB\-norgap\ \fR\fB\fIboolean\fR\fR \fB\-hgapres\ \fR\fB\fIstring\fR\fR \fB\-nohgap\ \fR\fB\fIboolean\fR\fR [\fB\-maxdiv\ \fR\fB\fIinteger\fR\fR] \fB\-outseq\ \fR\fB\fIseqoutset\fR\fR \fB\-dendoutfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBemma\fR\ 'u \fBemma\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBemma\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Multiple" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-onlydend\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-dend\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-dendfile\fR \fIinfile\fR .RS 4 .RE .PP \fB\-slow\fR \fItoggle\fR .RS 4 A distance is calculated between every pair of sequences and these are used to construct the dendrogram which guides the final multiple alignment\&. The scores are calculated from separate pairwise alignments\&. These can be calculated using 2 methods: dynamic programming (slow but accurate) or by the method of Wilbur and Lipman (extremely fast but approximate)\&. The slow\-accurate method is fine for short sequences but will be VERY SLOW for many (e\&.g\&. >100) long (e\&.g\&. >1000 residue) sequences\&. Default value: Y .RE .SS "Pairwise align options" .PP \fB\-pwmatrix\fR \fIlist\fR .RS 4 The scoring table which describes the similarity of each amino acid to each other\&. There are three \*(Aqin\-built\*(Aq series of weight matrices offered\&. Each consists of several matrices which work differently at different evolutionary distances\&. To see the exact details, read the documentation\&. Crudely, we store several matrices in memory, spanning the full range of amino acid distance (from almost identical sequences to highly divergent ones)\&. For very similar sequences, it is best to use a strict weight matrix which only gives a high score to identities and the most favoured conservative substitutions\&. For more divergent sequences, it is appropriate to use \*(Aqsofter\*(Aq matrices which give a high score to many other frequent substitutions\&. 1) BLOSUM (Henikoff)\&. These matrices appear to be the best available for carrying out data base similarity (homology searches)\&. The matrices used are: Blosum80, 62, 45 and 30\&. 2) PAM (Dayhoff)\&. These have been extremely widely used since the late \*(Aq70s\&. We use the PAM 120, 160, 250 and 350 matrices\&. 3) GONNET \&. These matrices were derived using almost the same procedure as the Dayhoff one (above) but are much more up to date and are based on a far larger data set\&. They appear to be more sensitive than the Dayhoff series\&. We use the GONNET 40, 80, 120, 160, 250 and 350 matrices\&. We also supply an identity matrix which gives a score of 1\&.0 to two identical amino acids and a score of zero otherwise\&. This matrix is not very useful\&. Default value: b .RE .PP \fB\-pwdnamatrix\fR \fIlist\fR .RS 4 The scoring table which describes the scores assigned to matches and mismatches (including IUB ambiguity codes)\&. Default value: i .RE .PP \fB\-usermatrix\fR \fIvariable\fR .RS 4 .RE .PP \fB\-pairwisedatafile\fR \fIinfile\fR .RS 4 .RE .SS "Matrix options" .PP \fB\-matrix\fR \fIlist\fR .RS 4 This gives a menu where you are offered a choice of weight matrices\&. The default for proteins is the PAM series derived by Gonnet and colleagues\&. Note, a series is used! The actual matrix that is used depends on how similar the sequences to be aligned at this alignment step are\&. Different matrices work differently at each evolutionary distance\&. There are three \*(Aqin\-built\*(Aq series of weight matrices offered\&. Each consists of several matrices which work differently at different evolutionary distances\&. To see the exact details, read the documentation\&. Crudely, we store several matrices in memory, spanning the full range of amino acid distance (from almost identical sequences to highly divergent ones)\&. For very similar sequences, it is best to use a strict weight matrix which only gives a high score to identities and the most favoured conservative substitutions\&. For more divergent sequences, it is appropriate to use \*(Aqsofter\*(Aq matrices which give a high score to many other frequent substitutions\&. 1) BLOSUM (Henikoff)\&. These matrices appear to be the best available for carrying out data base similarity (homology searches)\&. The matrices used are: Blosum80, 62, 45 and 30\&. 2) PAM (Dayhoff)\&. These have been extremely widely used since the late \*(Aq70s\&. We use the PAM 120, 160, 250 and 350 matrices\&. 3) GONNET \&. These matrices were derived using almost the same procedure as the Dayhoff one (above) but are much more up to date and are based on a far larger data set\&. They appear to be more sensitive than the Dayhoff series\&. We use the GONNET 40, 80, 120, 160, 250 and 350 matrices\&. We also supply an identity matrix which gives a score of 1\&.0 to two identical amino acids and a score of zero otherwise\&. This matrix is not very useful\&. Alternatively, you can read in your own (just one matrix, not a series)\&. Default value: b .RE .PP \fB\-usermamatrix\fR \fIvariable\fR .RS 4 .RE .PP \fB\-dnamatrix\fR \fIlist\fR .RS 4 This gives a menu where a single matrix (not a series) can be selected\&. Default value: i .RE .PP \fB\-umamatrix\fR \fIvariable\fR .RS 4 .RE .PP \fB\-mamatrixfile\fR \fIinfile\fR .RS 4 .RE .SS "Additional section" .SS "Slow align options" .PP \fB\-pwgapopen\fR \fIfloat\fR .RS 4 The penalty for opening a gap in the pairwise alignments\&. Default value: 10\&.0 .RE .PP \fB\-pwgapextend\fR \fIfloat\fR .RS 4 The penalty for extending a gap by 1 residue in the pairwise alignments\&. Default value: 0\&.1 .RE .SS "Fast align options" .PP \fB\-ktup\fR \fIinteger\fR .RS 4 This is the size of exactly matching fragment that is used\&. INCREASE for speed (max= 2 for proteins; 4 for DNA), DECREASE for sensitivity\&. For longer sequences (e\&.g\&. >1000 residues) you may need to increase the default\&. Default value: @($(acdprotein)?1:2) .RE .PP \fB\-gapw\fR \fIinteger\fR .RS 4 This is a penalty for each gap in the fast alignments\&. It has little affect on the speed or sensitivity except for extreme values\&. Default value: @($(acdprotein)?3:5) .RE .PP \fB\-topdiags\fR \fIinteger\fR .RS 4 The number of k\-tuple matches on each diagonal (in an imaginary dot\-matrix plot) is calculated\&. Only the best ones (with most matches) are used in the alignment\&. This parameter specifies how many\&. Decrease for speed; increase for sensitivity\&. Default value: @($(acdprotein)?5:4) .RE .PP \fB\-window\fR \fIinteger\fR .RS 4 This is the number of diagonals around each of the \*(Aqbest\*(Aq diagonals that will be used\&. Decrease for speed; increase for sensitivity\&. Default value: @($(acdprotein)?5:4) .RE .PP \fB\-nopercent\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Gap options" .PP \fB\-gapopen\fR \fIfloat\fR .RS 4 The penalty for opening a gap in the alignment\&. Increasing the gap opening penalty will make gaps less frequent\&. Default value: 10\&.0 .RE .PP \fB\-gapextend\fR \fIfloat\fR .RS 4 The penalty for extending a gap by 1 residue\&. Increasing the gap extension penalty will make gaps shorter\&. Terminal gaps are not penalised\&. Default value: 5\&.0 .RE .PP \fB\-endgaps\fR \fIboolean\fR .RS 4 End gap separation: treats end gaps just like internal gaps for the purposes of avoiding gaps that are too close (set by \*(Aqgap separation distance\*(Aq)\&. If you turn this off, end gaps will be ignored for this purpose\&. This is useful when you wish to align fragments where the end gaps are not biologically meaningful\&. Default value: Y .RE .PP \fB\-gapdist\fR \fIinteger\fR .RS 4 Gap separation distance: tries to decrease the chances of gaps being too close to each other\&. Gaps that are less than this distance apart are penalised more than other gaps\&. This does not prevent close gaps; it makes them less frequent, promoting a block\-like appearance of the alignment\&. Default value: 8 .RE .PP \fB\-norgap\fR \fIboolean\fR .RS 4 Residue specific penalties: amino acid specific gap penalties that reduce or increase the gap opening penalties at each position in the alignment or sequence\&. As an example, positions that are rich in glycine are more likely to have an adjacent gap than positions that are rich in valine\&. Default value: N .RE .PP \fB\-hgapres\fR \fIstring\fR .RS 4 This is a set of the residues \*(Aqconsidered\*(Aq to be hydrophilic\&. It is used when introducing Hydrophilic gap penalties\&. Default value: GPSNDQEKR .RE .PP \fB\-nohgap\fR \fIboolean\fR .RS 4 Hydrophilic gap penalties: used to increase the chances of a gap within a run (5 or more residues) of hydrophilic amino acids; these are likely to be loop or random coil regions where gaps are more common\&. The residues that are \*(Aqconsidered\*(Aq to be hydrophilic are set by \*(Aq\-hgapres\*(Aq\&. Default value: N .RE .PP \fB\-maxdiv\fR \fIinteger\fR .RS 4 This switch, delays the alignment of the most distantly related sequences until after the most closely related sequences have been aligned\&. The setting shows the percent identity level required to delay the addition of a sequence; sequences that are less identical than this level to any other sequences will be aligned later\&. Default value: 30 .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqoutset\fR .RS 4 .RE .PP \fB\-dendoutfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP emma is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/maskfeat.1e0000644000000000000000000000775412214054043013013 0ustar '\" t .\" Title: MASKFEAT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "MASKFEAT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" maskfeat \- Write a sequence with masked features .SH "SYNOPSIS" .HP \w'\fBmaskfeat\fR\ 'u \fBmaskfeat\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-type\ \fR\fB\fIstring\fR\fR] [\fB\-tolower\ \fR\fB\fItoggle\fR\fR] \fB\-maskchar\ \fR\fB\fIstring\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR .HP \w'\fBmaskfeat\fR\ 'u \fBmaskfeat\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBmaskfeat\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit,Feature tables" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Additional section" .PP \fB\-type\fR \fIstring\fR .RS 4 By default any feature in the feature table with a type starting \*(Aqrepeat\*(Aq is masked\&. You can set this to be any feature type you wish to mask\&. See http://www\&.ebi\&.ac\&.uk/embl/WebFeat/ for a list of the EMBL feature types and see Appendix A of the Swissprot user manual in http://www\&.expasy\&.org/sprot/userman\&.html for a list of the Swissprot feature types\&. The type may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to mask more than one type, separate their names with spaces or commas, eg: *UTR repeat* Default value: repeat* .RE .PP \fB\-tolower\fR \fItoggle\fR .RS 4 The region can be \*(Aqmasked\*(Aq by converting the sequence characters to lower\-case, some non\-EMBOSS programs e\&.g\&. fasta can interpret this as a masked region\&. The sequence is unchanged apart from the case change\&. You might like to ensure that the whole sequence is in upper\-case before masking the specified regions to lower\-case by using the \*(Aq\-supper\*(Aq flag\&. Default value: N .RE .PP \fB\-maskchar\fR \fIstring\fR .RS 4 Character to use when masking\&. Default is \*(AqX\*(Aq for protein sequences, \*(AqN\*(Aq for nucleic sequences\&. If the mask character is set to be the SPACE character or a null character, then the sequence is \*(Aqmasked\*(Aq by changing it to lower\-case, just as with the \*(Aq\-lowercase\*(Aq flag\&. Default value: @($(acdprotein)?X:N) .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqout\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP maskfeat is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/isochore.1e0000644000000000000000000000540012214054043013015 0ustar '\" t .\" Title: ISOCHORE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ISOCHORE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" isochore \- Plots isochores in DNA sequences .SH "SYNOPSIS" .HP \w'\fBisochore\fR\ 'u \fBisochore\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-window\ \fR\fB\fIinteger\fR\fR] [\fB\-shift\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR .HP \w'\fBisochore\fR\ 'u \fBisochore\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBisochore\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Composition" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .SS "Additional section" .PP \fB\-window\fR \fIinteger\fR .RS 4 Default value: 1000 .RE .PP \fB\-shift\fR \fIinteger\fR .RS 4 Default value: 100 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-graph\fR \fIxygraph\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP isochore is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/skipseq.1e0000644000000000000000000000515512214054043012670 0ustar '\" t .\" Title: SKIPSEQ .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SKIPSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" skipseq \- Reads and writes (returns) sequences, skipping first few .SH "SYNOPSIS" .HP \w'\fBskipseq\fR\ 'u \fBskipseq\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-skip\ \fR\fB\fIinteger\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBskipseq\fR\ 'u \fBskipseq\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBskipseq\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-feature\fR \fIboolean\fR .RS 4 .RE .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-skip\fR \fIinteger\fR .RS 4 .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP skipseq is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/freak.1e0000644000000000000000000000571212214054043012300 0ustar '\" t .\" Title: FREAK .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "FREAK" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" freak \- Generate residue/base frequency table or plot .SH "SYNOPSIS" .HP \w'\fBfreak\fR\ 'u \fBfreak\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-letters\ \fR\fB\fIstring\fR\fR [\fB\-step\ \fR\fB\fIinteger\fR\fR] [\fB\-window\ \fR\fB\fIinteger\fR\fR] \fB\-plot\ \fR\fB\fItoggle\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBfreak\fR\ 'u \fBfreak\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfreak\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Composition,Protein:Composition" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-seqall\fR \fIseqall\fR .RS 4 .RE .SS "Required section" .PP \fB\-letters\fR \fIstring\fR .RS 4 Default value: gc .RE .SS "Additional section" .PP \fB\-step\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-window\fR \fIinteger\fR .RS 4 Default value: 30 .RE .SS "Output section" .PP \fB\-plot\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-graph\fR \fIxygraph\fR .RS 4 .RE .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP freak is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/pepstats.1e0000644000000000000000000000573012214054043013053 0ustar '\" t .\" Title: PEPSTATS .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PEPSTATS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" pepstats \- Calculates statistics of protein properties .SH "SYNOPSIS" .HP \w'\fBpepstats\fR\ 'u \fBpepstats\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-aadata\ \fR\fB\fIdatafile\fR\fR \fB\-mwdata\ \fR\fB\fIdatafile\fR\fR \fB\-termini\ \fR\fB\fIboolean\fR\fR \fB\-mono\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBpepstats\fR\ 'u \fBpepstats\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBpepstats\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Composition,Protein:Properties" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-aadata\fR \fIdatafile\fR .RS 4 Amino acid properties Default value: Eamino\&.dat .RE .PP \fB\-mwdata\fR \fIdatafile\fR .RS 4 Molecular weight data for amino acids Default value: Emolwt\&.dat .RE .SS "Advanced section" .PP \fB\-termini\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-mono\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP pepstats is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/wordmatch.1e0000644000000000000000000000631412214054043013177 0ustar '\" t .\" Title: WORDMATCH .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "WORDMATCH" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" wordmatch \- Finds regions of identity (exact matches) of two sequences .SH "SYNOPSIS" .HP \w'\fBwordmatch\fR\ 'u \fBwordmatch\fR \fB\-asequence\ \fR\fB\fIseqset\fR\fR \fB\-bsequence\ \fR\fB\fIseqall\fR\fR \fB\-wordsize\ \fR\fB\fIinteger\fR\fR [\fB\-dumpalign\ \fR\fB\fItoggle\fR\fR] \fB\-outfile\ \fR\fB\fIalign\fR\fR [\fB\-logfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-dumpfeat\ \fR\fB\fItoggle\fR\fR] \fB\-aoutfeat\ \fR\fB\fIfeatout\fR\fR \fB\-boutfeat\ \fR\fB\fIfeatout\fR\fR .HP \w'\fBwordmatch\fR\ 'u \fBwordmatch\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBwordmatch\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Local" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-asequence\fR \fIseqset\fR .RS 4 .RE .PP \fB\-bsequence\fR \fIseqall\fR .RS 4 .RE .SS "Required section" .PP \fB\-wordsize\fR \fIinteger\fR .RS 4 Default value: 4 .RE .SS "Output section" .PP \fB\-dumpalign\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-outfile\fR \fIalign\fR .RS 4 .RE .PP \fB\-logfile\fR \fIoutfile\fR .RS 4 Statistics on distribution of kmers and matches Default value: wordmatch\&.log .RE .PP \fB\-dumpfeat\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-aoutfeat\fR \fIfeatout\fR .RS 4 .RE .PP \fB\-boutfeat\fR \fIfeatout\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP wordmatch is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/acdc.1e0000644000000000000000000000434512214054043012103 0ustar '\" t .\" Title: ACDC .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ACDC" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" acdc \- Test an application ACD file .SH "SYNOPSIS" .HP \w'\fBacdc\fR\ 'u \fBacdc\fR .HP \w'\fBacdc\fR\ 'u \fBacdc\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBacdc\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Acd,Data retrieval:Tool data" command group(s)\&. .SH "OPTIONS" .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP acdc is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/checktrans.1e0000644000000000000000000000647712214054043013346 0ustar '\" t .\" Title: CHECKTRANS .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "CHECKTRANS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" checktrans \- Reports STOP codons and ORF statistics of a protein .SH "SYNOPSIS" .HP \w'\fBchecktrans\fR\ 'u \fBchecktrans\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-orfml\ \fR\fB\fIinteger\fR\fR [\fB\-addlast\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR \fB\-outfeat\ \fR\fB\fIfeatout\fR\fR .HP \w'\fBchecktrans\fR\ 'u \fBchecktrans\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBchecktrans\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Gene finding,Nucleic:Translation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Required section" .PP \fB\-orfml\fR \fIinteger\fR .RS 4 Default value: 100 .RE .SS "Additional section" .PP \fB\-addlast\fR \fIboolean\fR .RS 4 An asterisk in the protein sequence indicates the position of a STOP codon\&. Checktrans assumes that all ORFs end in a STOP codon\&. Forcing the sequence to end with an asterisk, if there is not one there already, makes checktrans treat the end as a potential ORF\&. If an asterisk is added, it is not included in the reported count of STOPs\&. Default value: Y .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 Sequence file to hold output ORF sequences .RE .PP \fB\-outfeat\fR \fIfeatout\fR .RS 4 File for output features .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP checktrans is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/equicktandem.1e0000644000000000000000000000546612214054043013670 0ustar '\" t .\" Title: EQUICKTANDEM .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "EQUICKTANDEM" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" equicktandem \- Finds tandem repeats in nucleotide sequences .SH "SYNOPSIS" .HP \w'\fBequicktandem\fR\ 'u \fBequicktandem\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-maxrepeat\ \fR\fB\fIinteger\fR\fR \fB\-threshold\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR \fB\-origfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBequicktandem\fR\ 'u \fBequicktandem\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBequicktandem\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Repeats" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .SS "Required section" .PP \fB\-maxrepeat\fR \fIinteger\fR .RS 4 Default value: 600 .RE .PP \fB\-threshold\fR \fIinteger\fR .RS 4 Default value: 20 .RE .SS "Output section" .PP \fB\-outfile\fR \fIreport\fR .RS 4 .RE .PP \fB\-origfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP equicktandem is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/consambig.1e0000644000000000000000000000520012214054043013142 0ustar '\" t .\" Title: CONSAMBIG .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "CONSAMBIG" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" consambig \- Create an ambiguous consensus sequence from a multiple alignment .SH "SYNOPSIS" .HP \w'\fBconsambig\fR\ 'u \fBconsambig\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR [\fB\-name\ \fR\fB\fIstring\fR\fR] .HP \w'\fBconsambig\fR\ 'u \fBconsambig\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBconsambig\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Consensus" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqset\fR .RS 4 File containing a sequence alignment\&. .RE .SS "Additional section" .SS "Output section" .PP \fB\-outseq\fR \fIseqout\fR .RS 4 .RE .PP \fB\-name\fR \fIstring\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP consambig is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/pepwindow.1e0000644000000000000000000000547312214054043013230 0ustar '\" t .\" Title: PEPWINDOW .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PEPWINDOW" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" pepwindow \- Draw a hydropathy plot for a protein sequence .SH "SYNOPSIS" .HP \w'\fBpepwindow\fR\ 'u \fBpepwindow\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-datafile\ \fR\fB\fIdatafile\fR\fR] [\fB\-length\ \fR\fB\fIinteger\fR\fR] [\fB\-normalize\ \fR\fB\fIboolean\fR\fR] \fB\-graph\ \fR\fB\fIxygraph\fR\fR .HP \w'\fBpepwindow\fR\ 'u \fBpepwindow\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBpepwindow\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Properties" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .PP \fB\-datafile\fR \fIdatafile\fR .RS 4 Default value: Enakai\&.dat .RE .SS "Additional section" .PP \fB\-length\fR \fIinteger\fR .RS 4 Default value: 19 .RE .PP \fB\-normalize\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Output section" .PP \fB\-graph\fR \fIxygraph\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP pepwindow is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/dbgeturl.1e0000644000000000000000000000771412214054043013024 0ustar '\" t .\" Title: DBGETURL .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DBGETURL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" dbgeturl \- Retrieve links to database entries for a named database, data type and data identifier .SH "SYNOPSIS" .HP \w'\fBdbgeturl\fR\ 'u \fBdbgeturl\fR \fB\-database\ \fR\fB\fIstring\fR\fR \fB\-datatype\ \fR\fB\fIstring\fR\fR \fB\-identifier\ \fR\fB\fIstring\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] .HP \w'\fBdbgeturl\fR\ 'u \fBdbgeturl\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdbgeturl\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Misc" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-database\fR \fIstring\fR .RS 4 This is the name of a database from the catalogue of public databases in the EMBOSS data file DRCAT\&.dat\&. If you are unsure of the available databases use dbfind\&. If you have a database name but are not sure its valid, use isdbname\&. .RE .PP \fB\-datatype\fR \fIstring\fR .RS 4 This is the name of a retrievable datatype from the catalogue of public databases in the EMBOSS data file DRCAT\&.dat\&. The names are terms from the \*(Aqdata\*(Aq branch of the EDAM ontology, http://edamontology\&.sourceforge\&.net/\&. If you are unsure of the available retrievable datatypes for a given database, use dbtellquery\&. If you have a datatype name but are not sure its valid, use isdbdata\&. .RE .PP \fB\-identifier\fR \fIstring\fR .RS 4 This is a data identifier (e\&.g\&. a sequence accession number) that is used to specify the data (of type \*(Aqdatatype\*(Aq) to retrieve\&. If you\*(Aqre unsure of the data identifier(s) that are used for a given query (database/datatype) use dbtellquery\&. The types of data identifier are listed under the \*(AqData identifier\*(Aq branch of the EDAM ontology (http://edamontology\&.sourceforge\&.net/)\&. For example values, see the catalogue of public databases in the EMBOSS data file DRCAT\&.dat\&. If you have a data identifier but are unsure of its type, use idtell\&. .RE .SS "Required section" .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP dbgeturl is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/ontogetcommon.1e0000644000000000000000000000542212214054043014076 0ustar '\" t .\" Title: ONTOGETCOMMON .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ONTOGETCOMMON" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" ontogetcommon \- Get common ancestor for terms .SH "SYNOPSIS" .HP \w'\fBontogetcommon\fR\ 'u \fBontogetcommon\fR \fB\-oboterms\ \fR\fB\fIobo\fR\fR [\fB\-obsolete\ \fR\fB\fIboolean\fR\fR] \fB\-ontogetcommon\ \fR\fB\fIoutobo\fR\fR .HP \w'\fBontogetcommon\fR\ 'u \fBontogetcommon\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBontogetcommon\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology,Data retrieval:Ontology data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-oboterms\fR \fIobo\fR .RS 4 .RE .SS "Additional section" .PP \fB\-obsolete\fR \fIboolean\fR .RS 4 The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N .RE .SS "Advanced section" .SS "Output section" .PP \fB\-ontogetcommon\fR \fIoutobo\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP ontogetcommon is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/prophecy.1e0000644000000000000000000000627412214054043013045 0ustar '\" t .\" Title: PROPHECY .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PROPHECY" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" prophecy \- Create frequency matrix or profile from a multiple alignment .SH "SYNOPSIS" .HP \w'\fBprophecy\fR\ 'u \fBprophecy\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR \fB\-type\ \fR\fB\fIlist\fR\fR \fB\-datafile\ \fR\fB\fImatrixf\fR\fR \fB\-name\ \fR\fB\fIstring\fR\fR \fB\-threshold\ \fR\fB\fIinteger\fR\fR \fB\-open\ \fR\fB\fIfloat\fR\fR \fB\-extension\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBprophecy\fR\ 'u \fBprophecy\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBprophecy\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Profiles,Protein:Profiles" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqset\fR .RS 4 .RE .PP \fB\-type\fR \fIlist\fR .RS 4 Default value: F .RE .PP \fB\-datafile\fR \fImatrixf\fR .RS 4 Default value: @($(type) = G: Epprofile H: EBLOSUM62 F: EBLOSUM62) .RE .SS "Required section" .PP \fB\-name\fR \fIstring\fR .RS 4 Default value: mymatrix .RE .SS "Profile type specific options" .PP \fB\-threshold\fR \fIinteger\fR .RS 4 Default value: 75 .RE .SS "Gap options" .PP \fB\-open\fR \fIfloat\fR .RS 4 Default value: 3\&.0 .RE .PP \fB\-extension\fR \fIfloat\fR .RS 4 Default value: 0\&.3 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP prophecy is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/splitter.1e0000644000000000000000000000557112214054043013061 0ustar '\" t .\" Title: SPLITTER .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SPLITTER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" splitter \- Split sequence(s) into smaller sequences .SH "SYNOPSIS" .HP \w'\fBsplitter\fR\ 'u \fBsplitter\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-size\ \fR\fB\fIinteger\fR\fR] [\fB\-overlap\ \fR\fB\fIinteger\fR\fR] \fB\-addoverlap\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBsplitter\fR\ 'u \fBsplitter\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBsplitter\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-feature\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Additional section" .PP \fB\-size\fR \fIinteger\fR .RS 4 Default value: 10000 .RE .PP \fB\-overlap\fR \fIinteger\fR .RS 4 .RE .SS "Advanced section" .PP \fB\-addoverlap\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP splitter is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/est2genome.1e0000644000000000000000000001277012214054043013262 0ustar '\" t .\" Title: EST2GENOME .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "EST2GENOME" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" est2genome \- Align EST sequences to genomic DNA sequence .SH "SYNOPSIS" .HP \w'\fBest2genome\fR\ 'u \fBest2genome\fR \fB\-estsequence\ \fR\fB\fIseqall\fR\fR \fB\-genomesequence\ \fR\fB\fIsequence\fR\fR [\fB\-match\ \fR\fB\fIinteger\fR\fR] [\fB\-mismatch\ \fR\fB\fIinteger\fR\fR] [\fB\-gappenalty\ \fR\fB\fIinteger\fR\fR] [\fB\-intronpenalty\ \fR\fB\fIinteger\fR\fR] [\fB\-splicepenalty\ \fR\fB\fIinteger\fR\fR] [\fB\-minscore\ \fR\fB\fIinteger\fR\fR] \fB\-reverse\ \fR\fB\fIboolean\fR\fR \fB\-usesplice\ \fR\fB\fIboolean\fR\fR \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-best\ \fR\fB\fIboolean\fR\fR \fB\-space\ \fR\fB\fIfloat\fR\fR \fB\-shuffle\ \fR\fB\fIinteger\fR\fR \fB\-seed\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-align\ \fR\fB\fIboolean\fR\fR \fB\-width\ \fR\fB\fIinteger\fR\fR .HP \w'\fBest2genome\fR\ 'u \fBest2genome\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBest2genome\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Global" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-estsequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-genomesequence\fR \fIsequence\fR .RS 4 .RE .SS "Additional section" .PP \fB\-match\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-mismatch\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-gappenalty\fR \fIinteger\fR .RS 4 Cost for deleting a single base in either sequence, excluding introns Default value: 2 .RE .PP \fB\-intronpenalty\fR \fIinteger\fR .RS 4 Cost for an intron, independent of length\&. Default value: 40 .RE .PP \fB\-splicepenalty\fR \fIinteger\fR .RS 4 Cost for an intron, independent of length and starting/ending on donor\-acceptor sites Default value: 20 .RE .PP \fB\-minscore\fR \fIinteger\fR .RS 4 Exclude alignments with scores below this threshold score\&. Default value: 30 .RE .SS "Advanced section" .PP \fB\-reverse\fR \fIboolean\fR .RS 4 Reverse the orientation of the EST sequence .RE .PP \fB\-usesplice\fR \fIboolean\fR .RS 4 Use donor and acceptor splice sites\&. If you want to ignore donor\-acceptor sites then set this to be false\&. Default value: Y .RE .PP \fB\-mode\fR \fIlist\fR .RS 4 This determines the comparison mode\&. The default value is \*(Aqboth\*(Aq, in which case both strands of the est are compared assuming a forward gene direction (ie GT/AG splice sites), and the best comparison redone assuming a reversed (CT/AC) gene splicing direction\&. The other allowed modes are \*(Aqforward\*(Aq, when just the forward strand is searched, and \*(Aqreverse\*(Aq, ditto for the reverse strand\&. Default value: both .RE .PP \fB\-best\fR \fIboolean\fR .RS 4 You can print out all comparisons instead of just the best one by setting this to be false\&. Default value: Y .RE .PP \fB\-space\fR \fIfloat\fR .RS 4 For linear\-space recursion\&. If product of sequence lengths divided by 4 exceeds this then a divide\-and\-conquer strategy is used to control the memory requirements\&. In this way very long sequences can be aligned\&. If you have a machine with plenty of memory you can raise this parameter (but do not exceed the machine\*(Aqs physical RAM) Default value: 10\&.0 .RE .PP \fB\-shuffle\fR \fIinteger\fR .RS 4 .RE .PP \fB\-seed\fR \fIinteger\fR .RS 4 Default value: 20825 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-align\fR \fIboolean\fR .RS 4 Show the alignment\&. The alignment includes the first and last 5 bases of each intron, together with the intron width\&. The direction of splicing is indicated by angle brackets (forward or reverse) or ???? (unknown)\&. .RE .PP \fB\-width\fR \fIinteger\fR .RS 4 Default value: 50 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP est2genome is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/wosstopic.1e0000644000000000000000000001603112214054043013236 0ustar '\" t .\" Title: WOSSTOPIC .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "WOSSTOPIC" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" wosstopic \- Finds programs by EDAM topic .SH "SYNOPSIS" .HP \w'\fBwosstopic\fR\ 'u \fBwosstopic\fR \fB\-identifier\ \fR\fB\fIstring\fR\fR [\fB\-explode\ \fR\fB\fIboolean\fR\fR] [\fB\-showkeywords\ \fR\fB\fIboolean\fR\fR] \fB\-sensitive\ \fR\fB\fIboolean\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-emboss\ \fR\fB\fIboolean\fR\fR \fB\-embassy\ \fR\fB\fIboolean\fR\fR \fB\-showembassy\ \fR\fB\fIstring\fR\fR \fB\-colon\ \fR\fB\fIboolean\fR\fR \fB\-gui\ \fR\fB\fIboolean\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fItoggle\fR\fR] [\fB\-groups\ \fR\fB\fIboolean\fR\fR] [\fB\-alphabetic\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBwosstopic\fR\ 'u \fBwosstopic\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBwosstopic\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Documentation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-identifier\fR \fIstring\fR .RS 4 .RE .SS "Additional section" .PP \fB\-explode\fR \fIboolean\fR .RS 4 The groups that EMBOSS applications belong to have two forms, exploded and not exploded\&. The exploded group names are more numerous and often vaguely phrased than the non\-exploded ones\&. The exploded names are formed from definitions of the group names that start like NAME1:NAME2 and which are then expanded into many combinations of the names as: \*(AqNAME1\*(Aq, \*(AqNAME2\*(Aq, \*(AqNAME1 NAME2\*(Aq, NAME2 NAME1\*(Aq\&. The non\-expanded names are simply like: \*(AqNAME1 NAME2\*(Aq\&. Default value: N .RE .PP \fB\-showkeywords\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Advanced section" .PP \fB\-sensitive\fR \fIboolean\fR .RS 4 By default, the query keywords are matched against the EDAM term names (and synonyms) only\&. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches\&. Default value: N .RE .PP \fB\-subclasses\fR \fIboolean\fR .RS 4 Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: Y .RE .PP \fB\-obsolete\fR \fIboolean\fR .RS 4 The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N .RE .PP \fB\-emboss\fR \fIboolean\fR .RS 4 If you use this option then EMBOSS program documentation will be searched\&. If this option is set to be false, then only the EMBASSY programs will be searched (if the \-embassy option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y .RE .PP \fB\-embassy\fR \fIboolean\fR .RS 4 If you use this option then EMBASSY program documentation will be searched\&. If this option is set to be false, then only the EMBOSS programs will be searched (if the \-emboss option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y .RE .PP \fB\-showembassy\fR \fIstring\fR .RS 4 If you use this option then this EMBASSY package program documentation will be searched\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme .RE .PP \fB\-colon\fR \fIboolean\fR .RS 4 The groups that EMBOSS applications belong to up to two levels, for example the primary group \*(AqALIGNMENT\*(Aq has several sub\-groups, or second\-level groups, e\&.g\&.: CONSENSUS, DIFFERENCES, DOT PLOTS, GLOBAL, LOCAL, MULTIPLE\&. To aid programs that parse the output of wossname that require the names of these subgroups, a colon \*(Aq:\*(Aq will be placed between the first and second level of the group name if this option is true\&. Note: This does not apply if the group names have been exploded with the \*(Aqexplode\*(Aq option\&. Default value: N .RE .PP \fB\-gui\fR \fIboolean\fR .RS 4 This option is intended to help those who are designing Graphical User Interfaces to the EMBOSS applications\&. Some EMBOSS programs are inappropriate for running in a GUI, these include other menu programs and interactive editors\&. This option allows you to only report those programs that can be run from a GUI Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .SS "Html section" .PP \fB\-html\fR \fItoggle\fR .RS 4 If you are sending the output to a file, this will format it for displaying as a table in a WWW document\&. Default value: N .RE .PP \fB\-groups\fR \fIboolean\fR .RS 4 If you use this option, then only the group names will be output to the file Default value: N .RE .PP \fB\-alphabetic\fR \fIboolean\fR .RS 4 If you use this option, then you will get a single list of the program names and descriptions instead of the programs being listed in their functional groups\&. Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP wosstopic is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/martquery.1e0000644000000000000000000000606012214054043013236 0ustar '\" t .\" Title: MARTQUERY .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "MARTQUERY" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" martquery \- Perform a biomart query .SH "SYNOPSIS" .HP \w'\fBmartquery\fR\ 'u \fBmartquery\fR \fB\-dataset\ \fR\fB\fIstring\fR\fR \fB\-attributes\ \fR\fB\fIstring\fR\fR \fB\-filters\ \fR\fB\fIstring\fR\fR \fB\-host\ \fR\fB\fIstring\fR\fR \fB\-path\ \fR\fB\fIstring\fR\fR \fB\-port\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBmartquery\fR\ 'u \fBmartquery\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBmartquery\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-dataset\fR \fIstring\fR .RS 4 Default value: drerio_gene_ensembl .RE .PP \fB\-attributes\fR \fIstring\fR .RS 4 Default value: ensembl_gene_id,ensembl_transcript_id .RE .PP \fB\-filters\fR \fIstring\fR .RS 4 Default value: with_transmembrane_domain .RE .SS "Advanced section" .PP \fB\-host\fR \fIstring\fR .RS 4 Default value: www\&.biomart\&.org .RE .PP \fB\-path\fR \fIstring\fR .RS 4 Default value: /biomart/martservice .RE .PP \fB\-port\fR \fIinteger\fR .RS 4 Default value: 80 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP martquery is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/needle.1e0000644000000000000000000001161012214054043012436 0ustar '\" t .\" Title: NEEDLE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "NEEDLE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" needle \- Needleman\-Wunsch global alignment of two sequences .SH "SYNOPSIS" .HP \w'\fBneedle\fR\ 'u \fBneedle\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIseqall\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] \fB\-gapopen\ \fR\fB\fIfloat\fR\fR \fB\-gapextend\ \fR\fB\fIfloat\fR\fR [\fB\-endweight\ \fR\fB\fIboolean\fR\fR] [\fB\-endopen\ \fR\fB\fIfloat\fR\fR] [\fB\-endextend\ \fR\fB\fIfloat\fR\fR] \fB\-brief\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIalign\fR\fR .HP \w'\fBneedle\fR\ 'u \fBneedle\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBneedle\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Global" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-asequence\fR \fIsequence\fR .RS 4 .RE .PP \fB\-bsequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-datafile\fR \fImatrixf\fR .RS 4 This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&. .RE .SS "Required section" .PP \fB\-gapopen\fR \fIfloat\fR .RS 4 The gap open penalty is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: @($(acdprotein)? 10\&.0 : 10\&.0 ) .RE .PP \fB\-gapextend\fR \fIfloat\fR .RS 4 The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps\&. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring\&. Default value: @($(acdprotein)? 0\&.5 : 0\&.5 ) .RE .SS "Additional section" .PP \fB\-endweight\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-endopen\fR \fIfloat\fR .RS 4 The end gap open penalty is the score taken away when an end gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: @($(acdprotein)? 10\&.0 : 10\&.0 ) .RE .PP \fB\-endextend\fR \fIfloat\fR .RS 4 The end gap extension, penalty is added to the end gap penalty for each base or residue in the end gap\&. This is how long end gaps are penalized\&. Default value: @($(acdprotein)? 0\&.5 : 0\&.5 ) .RE .SS "Output section" .PP \fB\-brief\fR \fIboolean\fR .RS 4 Brief identity and similarity Default value: Y .RE .PP \fB\-outfile\fR \fIalign\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP needle is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/dbiflat.1e0000644000000000000000000000744412214054043012621 0ustar '\" t .\" Title: DBIFLAT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DBIFLAT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" dbiflat \- Index a flat file database .SH "SYNOPSIS" .HP \w'\fBdbiflat\fR\ 'u \fBdbiflat\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-idformat\ \fR\fB\fIlist\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-filenames\ \fR\fB\fIstring\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-maxindex\ \fR\fB\fIinteger\fR\fR \fB\-sortoptions\ \fR\fB\fIstring\fR\fR \fB\-systemsort\ \fR\fB\fIboolean\fR\fR \fB\-cleanup\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR .HP \w'\fBdbiflat\fR\ 'u \fBdbiflat\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdbiflat\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-dbname\fR \fIstring\fR .RS 4 .RE .PP \fB\-idformat\fR \fIlist\fR .RS 4 Default value: SWISS .RE .PP \fB\-directory\fR \fIdirectory\fR .RS 4 Default value: \&. .RE .PP \fB\-filenames\fR \fIstring\fR .RS 4 Default value: *\&.dat .RE .SS "Required section" .PP \fB\-release\fR \fIstring\fR .RS 4 Default value: 0\&.0 .RE .PP \fB\-date\fR \fIstring\fR .RS 4 Default value: 00/00/00 .RE .SS "Advanced section" .PP \fB\-fields\fR \fIlist\fR .RS 4 Default value: acc .RE .PP \fB\-exclude\fR \fIstring\fR .RS 4 .RE .PP \fB\-maxindex\fR \fIinteger\fR .RS 4 .RE .PP \fB\-sortoptions\fR \fIstring\fR .RS 4 Sort options, typically \*(Aq\-T \&.\*(Aq to use current directory for work files and \*(Aq\-k 1,1\*(Aq to force GNU sort to use the first field Default value: \-T \&. \-k 1,1 .RE .PP \fB\-systemsort\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-cleanup\fR \fIboolean\fR .RS 4 Default value: Y .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-indexoutdir\fR \fIoutdir\fR .RS 4 Default value: \&. .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP dbiflat is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/wossoperation.1e0000644000000000000000000001610112214054043014116 0ustar '\" t .\" Title: WOSSOPERATION .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "WOSSOPERATION" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" wossoperation \- Finds programs by EDAM operation .SH "SYNOPSIS" .HP \w'\fBwossoperation\fR\ 'u \fBwossoperation\fR \fB\-identifier\ \fR\fB\fIstring\fR\fR [\fB\-explode\ \fR\fB\fIboolean\fR\fR] [\fB\-showkeywords\ \fR\fB\fIboolean\fR\fR] \fB\-sensitive\ \fR\fB\fIboolean\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-emboss\ \fR\fB\fIboolean\fR\fR \fB\-embassy\ \fR\fB\fIboolean\fR\fR \fB\-showembassy\ \fR\fB\fIstring\fR\fR \fB\-colon\ \fR\fB\fIboolean\fR\fR \fB\-gui\ \fR\fB\fIboolean\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fItoggle\fR\fR] [\fB\-groups\ \fR\fB\fIboolean\fR\fR] [\fB\-alphabetic\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBwossoperation\fR\ 'u \fBwossoperation\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBwossoperation\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Documentation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-identifier\fR \fIstring\fR .RS 4 .RE .SS "Additional section" .PP \fB\-explode\fR \fIboolean\fR .RS 4 The groups that EMBOSS applications belong to have two forms, exploded and not exploded\&. The exploded group names are more numerous and often vaguely phrased than the non\-exploded ones\&. The exploded names are formed from definitions of the group names that start like NAME1:NAME2 and which are then expanded into many combinations of the names as: \*(AqNAME1\*(Aq, \*(AqNAME2\*(Aq, \*(AqNAME1 NAME2\*(Aq, NAME2 NAME1\*(Aq\&. The non\-expanded names are simply like: \*(AqNAME1 NAME2\*(Aq\&. Default value: N .RE .PP \fB\-showkeywords\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Advanced section" .PP \fB\-sensitive\fR \fIboolean\fR .RS 4 By default, the query keywords are matched against the EDAM term names (and synonyms) only\&. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches\&. Default value: N .RE .PP \fB\-subclasses\fR \fIboolean\fR .RS 4 Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: Y .RE .PP \fB\-obsolete\fR \fIboolean\fR .RS 4 The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N .RE .PP \fB\-emboss\fR \fIboolean\fR .RS 4 If you use this option then EMBOSS program documentation will be searched\&. If this option is set to be false, then only the EMBASSY programs will be searched (if the \-embassy option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y .RE .PP \fB\-embassy\fR \fIboolean\fR .RS 4 If you use this option then EMBASSY program documentation will be searched\&. If this option is set to be false, then only the EMBOSS programs will be searched (if the \-emboss option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y .RE .PP \fB\-showembassy\fR \fIstring\fR .RS 4 If you use this option then this EMBASSY package program documentation will be searched\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme .RE .PP \fB\-colon\fR \fIboolean\fR .RS 4 The groups that EMBOSS applications belong to up to two levels, for example the primary group \*(AqALIGNMENT\*(Aq has several sub\-groups, or second\-level groups, e\&.g\&.: CONSENSUS, DIFFERENCES, DOT PLOTS, GLOBAL, LOCAL, MULTIPLE\&. To aid programs that parse the output of wossname that require the names of these subgroups, a colon \*(Aq:\*(Aq will be placed between the first and second level of the group name if this option is true\&. Note: This does not apply if the group names have been exploded with the \*(Aqexplode\*(Aq option\&. Default value: N .RE .PP \fB\-gui\fR \fIboolean\fR .RS 4 This option is intended to help those who are designing Graphical User Interfaces to the EMBOSS applications\&. Some EMBOSS programs are inappropriate for running in a GUI, these include other menu programs and interactive editors\&. This option allows you to only report those programs that can be run from a GUI Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .SS "Html section" .PP \fB\-html\fR \fItoggle\fR .RS 4 If you are sending the output to a file, this will format it for displaying as a table in a WWW document\&. Default value: N .RE .PP \fB\-groups\fR \fIboolean\fR .RS 4 If you use this option, then only the group names will be output to the file Default value: N .RE .PP \fB\-alphabetic\fR \fIboolean\fR .RS 4 If you use this option, then you will get a single list of the program names and descriptions instead of the programs being listed in their functional groups\&. Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP wossoperation is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/drfinddata.1e0000644000000000000000000000611712214054043013310 0ustar '\" t .\" Title: DRFINDDATA .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DRFINDDATA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" drfinddata \- Find public databases by data type .SH "SYNOPSIS" .HP \w'\fBdrfinddata\fR\ 'u \fBdrfinddata\fR \fB\-query\ \fR\fB\fIstring\fR\fR \fB\-sensitive\ \fR\fB\fIboolean\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-drfinddata\ \fR\fB\fIoutresource\fR\fR .HP \w'\fBdrfinddata\fR\ 'u \fBdrfinddata\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdrfinddata\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Data retrieval:Resource data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-query\fR \fIstring\fR .RS 4 .RE .SS "Additional section" .SS "Advanced section" .PP \fB\-sensitive\fR \fIboolean\fR .RS 4 By default, the query keywords are matched against the EDAM term names (and synonyms) only\&. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches\&. Default value: N .RE .PP \fB\-subclasses\fR \fIboolean\fR .RS 4 Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: Y .RE .SS "Output section" .PP \fB\-drfinddata\fR \fIoutresource\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP drfinddata is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/psiphi.1e0000644000000000000000000000554012214054043012503 0ustar '\" t .\" Title: PSIPHI .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PSIPHI" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" psiphi \- Calculates phi and psi torsion angles from protein coordinates .SH "SYNOPSIS" .HP \w'\fBpsiphi\fR\ 'u \fBpsiphi\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-chainnumber\ \fR\fB\fIinteger\fR\fR \fB\-startresiduenumber\ \fR\fB\fIinteger\fR\fR \fB\-finishresiduenumber\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR .HP \w'\fBpsiphi\fR\ 'u \fBpsiphi\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBpsiphi\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "protein:3D structure" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .SS "Required section" .PP \fB\-chainnumber\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-startresiduenumber\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-finishresiduenumber\fR \fIinteger\fR .RS 4 Default value: 1 .RE .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIreport\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP psiphi is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/xmltotext.1e0000644000000000000000000000621412214054043013256 0ustar '\" t .\" Title: XMLTOTEXT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "XMLTOTEXT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" xmltotext \- Convert an XML document to a plain text format .SH "SYNOPSIS" .HP \w'\fBxmltotext\fR\ 'u \fBxmltotext\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-type\ \fR\fB\fIlist\fR\fR \fB\-seq\ \fR\fB\fIlist\fR\fR \fB\-feat\ \fR\fB\fIlist\fR\fR \fB\-align\ \fR\fB\fIlist\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBxmltotext\fR\ 'u \fBxmltotext\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBxmltotext\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Misc" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .SS "Required section" .PP \fB\-type\fR \fIlist\fR .RS 4 You must specify the type of file content so that appropriate output format options may be generated\&. .RE .PP \fB\-seq\fR \fIlist\fR .RS 4 This option sets the format of a sequence output file\&. Default value: X .RE .PP \fB\-feat\fR \fIlist\fR .RS 4 This option sets the format of a sequence feature output file\&. Default value: X .RE .PP \fB\-align\fR \fIlist\fR .RS 4 This option sets the format of a sequence alignment output file\&. Default value: X .RE .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP xmltotext is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/eprimer3.1e0000644000000000000000000006710312214054043012740 0ustar '\" t .\" Title: EPRIMER3 .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "EPRIMER3" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" eprimer3 \- Picks PCR primers and hybridization oligos .SH "SYNOPSIS" .HP \w'\fBeprimer3\fR\ 'u \fBeprimer3\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-primer\ \fR\fB\fItoggle\fR\fR] \fB\-task\ \fR\fB\fIlist\fR\fR [\fB\-hybridprobe\ \fR\fB\fItoggle\fR\fR] \fB\-mishyblibraryfile\ \fR\fB\fIinfile\fR\fR \fB\-mispriminglibraryfile\ \fR\fB\fIinfile\fR\fR [\fB\-numreturn\ \fR\fB\fIinteger\fR\fR] [\fB\-includedregion\ \fR\fB\fIrange\fR\fR] [\fB\-targetregion\ \fR\fB\fIrange\fR\fR] [\fB\-excludedregion\ \fR\fB\fIrange\fR\fR] [\fB\-forwardinput\ \fR\fB\fIstring\fR\fR] [\fB\-reverseinput\ \fR\fB\fIstring\fR\fR] \fB\-gcclamp\ \fR\fB\fIinteger\fR\fR \fB\-osize\ \fR\fB\fIinteger\fR\fR \fB\-minsize\ \fR\fB\fIinteger\fR\fR \fB\-maxsize\ \fR\fB\fIinteger\fR\fR \fB\-otm\ \fR\fB\fIfloat\fR\fR \fB\-mintm\ \fR\fB\fIfloat\fR\fR \fB\-maxtm\ \fR\fB\fIfloat\fR\fR \fB\-maxdifftm\ \fR\fB\fIfloat\fR\fR \fB\-ogcpercent\ \fR\fB\fIfloat\fR\fR \fB\-mingc\ \fR\fB\fIfloat\fR\fR \fB\-maxgc\ \fR\fB\fIfloat\fR\fR \fB\-saltconc\ \fR\fB\fIfloat\fR\fR \fB\-dnaconc\ \fR\fB\fIfloat\fR\fR \fB\-maxpolyx\ \fR\fB\fIinteger\fR\fR \fB\-psizeopt\ \fR\fB\fIinteger\fR\fR \fB\-prange\ \fR\fB\fIrange\fR\fR \fB\-ptmopt\ \fR\fB\fIfloat\fR\fR \fB\-ptmmin\ \fR\fB\fIfloat\fR\fR \fB\-ptmmax\ \fR\fB\fIfloat\fR\fR \fB\-oexcludedregion\ \fR\fB\fIrange\fR\fR \fB\-oligoinput\ \fR\fB\fIstring\fR\fR \fB\-osizeopt\ \fR\fB\fIinteger\fR\fR \fB\-ominsize\ \fR\fB\fIinteger\fR\fR \fB\-omaxsize\ \fR\fB\fIinteger\fR\fR \fB\-otmopt\ \fR\fB\fIfloat\fR\fR \fB\-otmmin\ \fR\fB\fIfloat\fR\fR \fB\-otmmax\ \fR\fB\fIfloat\fR\fR \fB\-ogcopt\ \fR\fB\fIfloat\fR\fR \fB\-ogcmin\ \fR\fB\fIfloat\fR\fR \fB\-ogcmax\ \fR\fB\fIfloat\fR\fR \fB\-osaltconc\ \fR\fB\fIfloat\fR\fR \fB\-odnaconc\ \fR\fB\fIfloat\fR\fR \fB\-oanyself\ \fR\fB\fIfloat\fR\fR \fB\-oendself\ \fR\fB\fIfloat\fR\fR \fB\-opolyxmax\ \fR\fB\fIinteger\fR\fR \fB\-omishybmax\ \fR\fB\fIfloat\fR\fR \fB\-explainflag\ \fR\fB\fIboolean\fR\fR \fB\-fileflag\ \fR\fB\fIboolean\fR\fR \fB\-firstbaseindex\ \fR\fB\fIinteger\fR\fR \fB\-pickanyway\ \fR\fB\fIboolean\fR\fR \fB\-maxmispriming\ \fR\fB\fIfloat\fR\fR \fB\-pairmaxmispriming\ \fR\fB\fIfloat\fR\fR \fB\-numnsaccepted\ \fR\fB\fIinteger\fR\fR \fB\-selfany\ \fR\fB\fIfloat\fR\fR \fB\-selfend\ \fR\fB\fIfloat\fR\fR \fB\-maxendstability\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBeprimer3\fR\ 'u \fBeprimer3\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBeprimer3\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Primers" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 The sequence from which to choose primers\&. The sequence must be presented 5\*(Aq to 3\*(Aq .RE .PP \fB\-primer\fR \fItoggle\fR .RS 4 Tell EPrimer3 to pick primer(s) Default value: Y .RE .PP \fB\-task\fR \fIlist\fR .RS 4 Tell EPrimer3 what task to perform\&. Legal values are 1: \*(AqPick PCR primers\*(Aq, 2: \*(AqPick forward primer only\*(Aq, 3: \*(AqPick reverse primer only\*(Aq, 4: \*(AqNo primers needed\*(Aq\&. Default value: 1 .RE .PP \fB\-hybridprobe\fR \fItoggle\fR .RS 4 An \*(Aqinternal oligo\*(Aq is intended to be used as a hybridization probe (hyb probe) to detect the PCR product after amplification\&. Default value: N .RE .PP \fB\-mishyblibraryfile\fR \fIinfile\fR .RS 4 Similar to MISPRIMING\-LIBRARY, except that the event we seek to avoid is hybridization of the internal oligo to sequences in this library rather than priming from them\&. The file must be in (a slightly restricted) FASTA format (W\&. B\&. Pearson and D\&.J\&. Lipman, PNAS 85:8 pp 2444\-2448 [1988]); we briefly discuss the organization of this file below\&. If this parameter is specified then EPrimer3 locally aligns each candidate oligo against each library sequence and rejects those primers for which the local alignment score times a specified weight (see below) exceeds INTERNAL\-OLIGO\-MAX\-MISHYB\&. (The maximum value of the weight is arbitrarily set to 12\&.0\&.) Each sequence entry in the FASTA\-format file must begin with an \*(Aqid line\*(Aq that starts with \*(Aq>\*(Aq\&. The contents of the id line is \*(Aqslightly restricted\*(Aq in that EPrimer3 parses everything after any optional asterisk (\*(Aq*\*(Aq) as a floating point number to use as the weight mentioned above\&. If the id line contains no asterisk then the weight defaults to 1\&.0\&. The alignment scoring system used is the same as for calculating complementarity among oligos (e\&.g\&. SELF\-ANY)\&. The remainder of an entry contains the sequence as lines following the id line up until a line starting with \*(Aq>\*(Aq or the end of the file\&. Whitespace and newlines are ignored\&. Characters \*(AqA\*(Aq, \*(AqT\*(Aq, \*(AqG\*(Aq, \*(AqC\*(Aq, \*(Aqa\*(Aq, \*(Aqt\*(Aq, \*(Aqg\*(Aq, \*(Aqc\*(Aq are retained and any other character is converted to \*(AqN\*(Aq (with the consequence that any IUB / IUPAC codes for ambiguous bases are converted to \*(AqN\*(Aq)\&. There are no restrictions on line length\&. An empty value for this parameter indicates that no library should be used\&. .RE .PP \fB\-mispriminglibraryfile\fR \fIinfile\fR .RS 4 The name of a file containing a nucleotide sequence library of sequences to avoid amplifying (for example repetitive sequences, or possibly the sequences of genes in a gene family that should not be amplified\&.) The file must be in (a slightly restricted) FASTA format (W\&. B\&. Pearson and D\&.J\&. Lipman, PNAS 85:8 pp 2444\-2448 [1988]); we briefly discuss the organization of this file below\&. If this parameter is specified then EPrimer3 locally aligns each candidate primer against each library sequence and rejects those primers for which the local alignment score times a specified weight (see below) exceeds MAX\-MISPRIMING\&. (The maximum value of the weight is arbitrarily set to 100\&.0\&.) Each sequence entry in the FASTA\-format file must begin with an \*(Aqid line\*(Aq that starts with \*(Aq>\*(Aq\&. The contents of the id line is \*(Aqslightly restricted\*(Aq in that EPrimer3 parses everything after any optional asterisk (\*(Aq*\*(Aq) as a floating point number to use as the weight mentioned above\&. If the id line contains no asterisk then the weight defaults to 1\&.0\&. The alignment scoring system used is the same as for calculating complementarity among oligos (e\&.g\&. SELF\-ANY)\&. The remainder of an entry contains the sequence as lines following the id line up until a line starting with \*(Aq>\*(Aq or the end of the file\&. Whitespace and newlines are ignored\&. Characters \*(AqA\*(Aq, \*(AqT\*(Aq, \*(AqG\*(Aq, \*(AqC\*(Aq, \*(Aqa\*(Aq, \*(Aqt\*(Aq, \*(Aqg\*(Aq, \*(Aqc\*(Aq are retained and any other character is converted to \*(AqN\*(Aq (with the consequence that any IUB / IUPAC codes for ambiguous bases are converted to \*(AqN\*(Aq)\&. There are no restrictions on line length\&. An empty value for this parameter indicates that no repeat library should be used\&. .RE .SS "Additional section" .SS "Program options" .PP \fB\-numreturn\fR \fIinteger\fR .RS 4 The maximum number of primer pairs to return\&. Primer pairs returned are sorted by their \*(Aqquality\*(Aq, in other words by the value of the objective function (where a lower number indicates a better primer pair)\&. Caution: setting this parameter to a large value will increase running time\&. Default value: 5 .RE .SS "Sequence options" .PP \fB\-includedregion\fR \fIrange\fR .RS 4 A sub\-region of the given sequence in which to pick primers\&. For example, often the first dozen or so bases of a sequence are vector, and should be excluded from consideration\&. The value for this parameter has the form (start),(end) where (start) is the index of the first base to consider, and (end) is the last in the primer\-picking region\&. .RE .PP \fB\-targetregion\fR \fIrange\fR .RS 4 If one or more Targets is specified then a legal primer pair must flank at least one of them\&. A Target might be a simple sequence repeat site (for example a CA repeat) or a single\-base\-pair polymorphism\&. The value should be a space\-separated list of (start),(end) pairs where (start) is the index of the first base of a Target, and (end) is the last E\&.g\&. 50,51 requires primers to surround the 2 bases at positions 50 and 51\&. .RE .PP \fB\-excludedregion\fR \fIrange\fR .RS 4 Primer oligos may not overlap any region specified in this tag\&. The associated value must be a space\-separated list of (start),(end) pairs where (start) is the index of the first base of the excluded region, and and (end) is the last\&. This tag is useful for tasks such as excluding regions of low sequence quality or for excluding regions containing repetitive elements such as ALUs or LINEs\&. E\&.g\&. 401,407 68,70 forbids selection of primers in the 7 bases starting at 401 and the 3 bases at 68\&. .RE .PP \fB\-forwardinput\fR \fIstring\fR .RS 4 The sequence of a forward primer to check and around which to design reverse primers and optional internal oligos\&. Must be a substring of SEQUENCE\&. .RE .PP \fB\-reverseinput\fR \fIstring\fR .RS 4 The sequence of a reverse primer to check and around which to design forward primers and optional internal oligos\&. Must be a substring of the reverse strand of SEQUENCE\&. .RE .SS "Primer options" .PP \fB\-gcclamp\fR \fIinteger\fR .RS 4 Require the specified number of consecutive Gs and Cs at the 3\*(Aq end of both the forward and reverse primer\&. (This parameter has no effect on the internal oligo if one is requested\&.) .RE .PP \fB\-osize\fR \fIinteger\fR .RS 4 Optimum length (in bases) of a primer oligo\&. EPrimer3 will attempt to pick primers close to this length\&. Default value: 20 .RE .PP \fB\-minsize\fR \fIinteger\fR .RS 4 Minimum acceptable length of a primer\&. Must be greater than 0 and less than or equal to MAX\-SIZE\&. Default value: 18 .RE .PP \fB\-maxsize\fR \fIinteger\fR .RS 4 Maximum acceptable length (in bases) of a primer\&. Currently this parameter cannot be larger than 35\&. This limit is governed by the maximum oligo size for which EPrimer3\*(Aqs melting\-temperature is valid\&. Default value: 27 .RE .PP \fB\-otm\fR \fIfloat\fR .RS 4 Optimum melting temperature(Celsius) for a primer oligo\&. EPrimer3 will try to pick primers with melting temperatures are close to this temperature\&. The oligo melting temperature formula in EPrimer3 is that given in Rychlik, Spencer and Rhoads, Nucleic Acids Research, vol 18, num 21, pp 6409\-6412 and Breslauer, Frank, Bloecker and Marky, Proc\&. Natl\&. Acad\&. Sci\&. USA, vol 83, pp 3746\-3750\&. Please refer to the former paper for background discussion\&. Default value: 60\&.0 .RE .PP \fB\-mintm\fR \fIfloat\fR .RS 4 Minimum acceptable melting temperature(Celsius) for a primer oligo\&. Default value: 57\&.0 .RE .PP \fB\-maxtm\fR \fIfloat\fR .RS 4 Maximum acceptable melting temperature(Celsius) for a primer oligo\&. Default value: 63\&.0 .RE .PP \fB\-maxdifftm\fR \fIfloat\fR .RS 4 Maximum acceptable (unsigned) difference between the melting temperatures of the forward and reverse primers\&. Default value: 100\&.0 .RE .PP \fB\-ogcpercent\fR \fIfloat\fR .RS 4 Primer optimum GC percent\&. Default value: 50\&.0 .RE .PP \fB\-mingc\fR \fIfloat\fR .RS 4 Minimum allowable percentage of Gs and Cs in any primer\&. Default value: 20\&.0 .RE .PP \fB\-maxgc\fR \fIfloat\fR .RS 4 Maximum allowable percentage of Gs and Cs in any primer generated by Primer\&. Default value: 80\&.0 .RE .PP \fB\-saltconc\fR \fIfloat\fR .RS 4 The millimolar concentration of salt (usually KCl) in the PCR\&. EPrimer3 uses this argument to calculate oligo melting temperatures\&. Default value: 50\&.0 .RE .PP \fB\-dnaconc\fR \fIfloat\fR .RS 4 The nanomolar concentration of annealing oligos in the PCR\&. EPrimer3 uses this argument to calculate oligo melting temperatures\&. The default (50nM) works well with the standard protocol used at the Whitehead/MIT Center for Genome Research\-\-0\&.5 microliters of 20 micromolar concentration for each primer oligo in a 20 microliter reaction with 10 nanograms template, 0\&.025 units/microliter Taq polymerase in 0\&.1 mM each dNTP, 1\&.5mM MgCl2, 50mM KCl, 10mM Tris\-HCL (pH 9\&.3) using 35 cycles with an annealing temperature of 56 degrees Celsius\&. This parameter corresponds to \*(Aqc\*(Aq in Rychlik, Spencer and Rhoads\*(Aq equation (ii) (Nucleic Acids Research, vol 18, num 21) where a suitable value (for a lower initial concentration of template) is \*(Aqempirically determined\*(Aq\&. The value of this parameter is less than the actual concentration of oligos in the reaction because it is the concentration of annealing oligos, which in turn depends on the amount of template (including PCR product) in a given cycle\&. This concentration increases a great deal during a PCR; fortunately PCR seems quite robust for a variety of oligo melting temperatures\&. See ADVICE FOR PICKING PRIMERS\&. Default value: 50\&.0 .RE .PP \fB\-maxpolyx\fR \fIinteger\fR .RS 4 The maximum allowable length of a mononucleotide repeat in a primer, for example AAAAAA\&. Default value: 5 .RE .SS "Product options" .PP \fB\-psizeopt\fR \fIinteger\fR .RS 4 The optimum size for the PCR product\&. 0 indicates that there is no optimum product size\&. Default value: 200 .RE .PP \fB\-prange\fR \fIrange\fR .RS 4 The associated values specify the lengths of the product that the user wants the primers to create, and is a space separated list of elements of the form (x)\-(y) where an (x)\-(y) pair is a legal range of lengths for the product\&. For example, if one wants PCR products to be between 100 to 150 bases (inclusive) then one would set this parameter to 100\-150\&. If one desires PCR products in either the range from 100 to 150 bases or in the range from 200 to 250 bases then one would set this parameter to 100\-150 200\-250\&. EPrimer3 favors ranges to the left side of the parameter string\&. EPrimer3 will return legal primers pairs in the first range regardless the value of the objective function for these pairs\&. Only if there are an insufficient number of primers in the first range will EPrimer3 return primers in a subsequent range\&. Default value: 100\-300 .RE .PP \fB\-ptmopt\fR \fIfloat\fR .RS 4 The optimum melting temperature for the PCR product\&. 0 indicates that there is no optimum temperature\&. Default value: 0\&.0 .RE .PP \fB\-ptmmin\fR \fIfloat\fR .RS 4 The minimum allowed melting temperature of the amplicon\&. Please see the documentation on the maximum melting temperature of the product for details\&. Default value: \-1000000\&.0 .RE .PP \fB\-ptmmax\fR \fIfloat\fR .RS 4 The maximum allowed melting temperature of the amplicon\&. Product Tm is calculated using the formula from Bolton and McCarthy, PNAS 84:1390 (1962) as presented in Sambrook, Fritsch and Maniatis, Molecular Cloning, p 11\&.46 (1989, CSHL Press)\&. Tm = 81\&.5 + 16\&.6(log10([Na+])) + \&.41*(%GC) \- 600/length Where [Na+} is the molar sodium concentration, (%GC) is the percent of Gs and Cs in the sequence, and length is the length of the sequence\&. A similar formula is used by the prime primer selection program in GCG, which instead uses 675\&.0/length in the last term (after F\&. Baldino, Jr, M\&.\-F\&. Chesselet, and M\&.E\&. Lewis, Methods in Enzymology 168:766 (1989) eqn (1) on page 766 without the mismatch and formamide terms)\&. The formulas here and in Baldino et al\&. assume Na+ rather than K+\&. According to J\&.G\&. Wetmur, Critical Reviews in BioChem\&. and Mol\&. Bio\&. 26:227 (1991) 50 mM K+ should be equivalent in these formulae to \&.2 M Na+\&. EPrimer3 uses the same salt concentration value for calculating both the primer melting temperature and the oligo melting temperature\&. If you are planning to use the PCR product for hybridization later this behavior will not give you the Tm under hybridization conditions\&. Default value: 1000000\&.0 .RE .SS "Internal oligo input" .PP \fB\-oexcludedregion\fR \fIrange\fR .RS 4 Middle oligos may not overlap any region specified by this tag\&. The associated value must be a space\-separated list of (start),(end) pairs, where (start) is the index of the first base of an excluded region, and (end) is the last\&. Often one would make Target regions excluded regions for internal oligos\&. .RE .PP \fB\-oligoinput\fR \fIstring\fR .RS 4 The sequence of an internal oligo to check and around which to design forward and reverse primers\&. Must be a substring of SEQUENCE\&. .RE .SS "Internal oligo options" .PP \fB\-osizeopt\fR \fIinteger\fR .RS 4 Optimum length (in bases) of an internal oligo\&. EPrimer3 will attempt to pick primers close to this length\&. Default value: 20 .RE .PP \fB\-ominsize\fR \fIinteger\fR .RS 4 Minimum acceptable length of an internal oligo\&. Must be greater than 0 and less than or equal to INTERNAL\-OLIGO\-MAX\-SIZE\&. Default value: 18 .RE .PP \fB\-omaxsize\fR \fIinteger\fR .RS 4 Maximum acceptable length (in bases) of an internal oligo\&. Currently this parameter cannot be larger than 35\&. This limit is governed by maximum oligo size for which EPrimer3\*(Aqs melting\-temperature is valid\&. Default value: 27 .RE .PP \fB\-otmopt\fR \fIfloat\fR .RS 4 Optimum melting temperature (Celsius) for an internal oligo\&. EPrimer3 will try to pick oligos with melting temperatures that are close to this temperature\&. The oligo melting temperature formula in EPrimer3 is that given in Rychlik, Spencer and Rhoads, Nucleic Acids Research, vol 18, num 21, pp 6409\-6412 and Breslauer, Frank, Bloecker and Marky, Proc\&. Natl\&. Acad\&. Sci\&. USA, vol 83, pp 3746\-3750\&. Please refer to the former paper for background discussion\&. Default value: 60\&.0 .RE .PP \fB\-otmmin\fR \fIfloat\fR .RS 4 Minimum acceptable melting temperature(Celsius) for an internal oligo\&. Default value: 57\&.0 .RE .PP \fB\-otmmax\fR \fIfloat\fR .RS 4 Maximum acceptable melting temperature (Celsius) for an internal oligo\&. Default value: 63\&.0 .RE .PP \fB\-ogcopt\fR \fIfloat\fR .RS 4 Internal oligo optimum GC percent\&. Default value: 50\&.0 .RE .PP \fB\-ogcmin\fR \fIfloat\fR .RS 4 Minimum allowable percentage of Gs and Cs in an internal oligo\&. Default value: 20\&.0 .RE .PP \fB\-ogcmax\fR \fIfloat\fR .RS 4 Maximum allowable percentage of Gs and Cs in any internal oligo generated by Primer\&. Default value: 80\&.0 .RE .PP \fB\-osaltconc\fR \fIfloat\fR .RS 4 The millimolar concentration of salt (usually KCl) in the hybridization\&. EPrimer3 uses this argument to calculate internal oligo melting temperatures\&. Default value: 50\&.0 .RE .PP \fB\-odnaconc\fR \fIfloat\fR .RS 4 The nanomolar concentration of annealing internal oligo in the hybridization\&. Default value: 50\&.0 .RE .PP \fB\-oanyself\fR \fIfloat\fR .RS 4 The maximum allowable local alignment score when testing an internal oligo for (local) self\-complementarity\&. Local self\-complementarity is taken to predict the tendency of oligos to anneal to themselves The scoring system gives 1\&.00 for complementary bases, \-0\&.25 for a match of any base (or N) with an N, \-1\&.00 for a mismatch, and \-2\&.00 for a gap\&. Only single\-base\-pair gaps are allowed\&. For example, the alignment 5\*(Aq ATCGNA 3\*(Aq || | | 3\*(Aq TA\-CGT 5\*(Aq is allowed (and yields a score of 1\&.75), but the alignment 5\*(Aq ATCCGNA 3\*(Aq || | | 3\*(Aq TA\-\-CGT 5\*(Aq is not considered\&. Scores are non\-negative, and a score of 0\&.00 indicates that there is no reasonable local alignment between two oligos\&. Default value: 12\&.00 .RE .PP \fB\-oendself\fR \fIfloat\fR .RS 4 The maximum allowable 3\*(Aq\-anchored global alignment score when testing a single oligo for self\-complementarity\&. The scoring system is as for the Maximum Complementarity argument\&. In the examples above the scores are 7\&.00 and 6\&.00 respectively\&. Scores are non\-negative, and a score of 0\&.00 indicates that there is no reasonable 3\*(Aq\-anchored global alignment between two oligos\&. In order to estimate 3\*(Aq\-anchored global alignments for candidate oligos, Primer assumes that the sequence from which to choose oligos is presented 5\*(Aq to 3\*(Aq\&. INTERNAL\-OLIGO\-SELF\-END is meaningless when applied to internal oligos used for hybridization\-based detection, since primer\-dimer will not occur\&. We recommend that INTERNAL\-OLIGO\-SELF\-END be set at least as high as INTERNAL\-OLIGO\-SELF\-ANY\&. Default value: 12\&.00 .RE .PP \fB\-opolyxmax\fR \fIinteger\fR .RS 4 The maximum allowable length of an internal oligo mononucleotide repeat, for example AAAAAA\&. Default value: 5 .RE .PP \fB\-omishybmax\fR \fIfloat\fR .RS 4 Similar to MAX\-MISPRIMING except that this parameter applies to the similarity of candidate internal oligos to the library specified in INTERNAL\-OLIGO\-MISHYB\-LIBRARY\&. Default value: 12\&.0 .RE .SS "Advanced section" .PP \fB\-explainflag\fR \fIboolean\fR .RS 4 If this flag is true, produce LEFT\-EXPLAIN, RIGHT\-EXPLAIN, and INTERNAL\-OLIGO\-EXPLAIN output tags, which are intended to provide information on the number of oligos and primer pairs that EPrimer3 examined, and statistics on the number discarded for various reasons\&. Default value: N .RE .PP \fB\-fileflag\fR \fIboolean\fR .RS 4 If the associated value is true, then EPrimer3 creates two output files for each input SEQUENCE\&. File (sequence\-id)\&.for lists all acceptable forward primers for (sequence\-id), and (sequence\-id)\&.rev lists all acceptable reverse primers for (sequence\-id), where (sequence\-id) is the value of the SEQUENCE\-ID tag (which must be supplied)\&. In addition, if the input tag TASK is 1 or 4, EPrimer3 produces a file (sequence\-id)\&.int, which lists all acceptable internal oligos\&. Default value: N .RE .PP \fB\-firstbaseindex\fR \fIinteger\fR .RS 4 This parameter is the index of the first base in the input sequence\&. For input and output using 1\-based indexing (such as that used in GenBank and to which many users are accustomed) set this parameter to 1\&. For input and output using 0\-based indexing set this parameter to 0\&. (This parameter also affects the indexes in the contents of the files produced when the primer file flag is set\&.) Default value: 1 .RE .PP \fB\-pickanyway\fR \fIboolean\fR .RS 4 If true pick a primer pair even if LEFT\-INPUT, RIGHT\-INPUT, or INTERNAL\-OLIGO\-INPUT violates specific constraints\&. Default value: N .RE .PP \fB\-maxmispriming\fR \fIfloat\fR .RS 4 The maximum allowed weighted similarity with any sequence in MISPRIMING\-LIBRARY\&. Default value: 12\&.00 .RE .PP \fB\-pairmaxmispriming\fR \fIfloat\fR .RS 4 The maximum allowed sum of weighted similarities of a primer pair (one similarity for each primer) with any single sequence in MISPRIMING\-LIBRARY\&. Default value: 24\&.00 .RE .PP \fB\-numnsaccepted\fR \fIinteger\fR .RS 4 Maximum number of unknown bases (N) allowable in any primer\&. .RE .PP \fB\-selfany\fR \fIfloat\fR .RS 4 The maximum allowable local alignment score when testing a single primer for (local) self\-complementarity and the maximum allowable local alignment score when testing for complementarity between forward and reverse primers\&. Local self\-complementarity is taken to predict the tendency of primers to anneal to each other without necessarily causing self\-priming in the PCR\&. The scoring system gives 1\&.00 for complementary bases, \-0\&.25 for a match of any base (or N) with an N, \-1\&.00 for a mismatch, and \-2\&.00 for a gap\&. Only single\-base\-pair gaps are allowed\&. For example, the alignment 5\*(Aq ATCGNA 3\*(Aq \&.\&.\&.|| | | 3\*(Aq TA\-CGT 5\*(Aq is allowed (and yields a score of 1\&.75), but the alignment 5\*(Aq ATCCGNA 3\*(Aq \&.\&.\&.|| | | 3\*(Aq TA\-\-CGT 5\*(Aq is not considered\&. Scores are non\-negative, and a score of 0\&.00 indicates that there is no reasonable local alignment between two oligos\&. Default value: 8\&.00 .RE .PP \fB\-selfend\fR \fIfloat\fR .RS 4 The maximum allowable 3\*(Aq\-anchored global alignment score when testing a single primer for self\-complementarity, and the maximum allowable 3\*(Aq\-anchored global alignment score when testing for complementarity between forward and reverse primers\&. The 3\*(Aq\-anchored global alignment score is taken to predict the likelihood of PCR\-priming primer\-dimers, for example 5\*(Aq ATGCCCTAGCTTCCGGATG 3\*(Aq \&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.||| ||||| \&.\&.\&.\&.\&.\&.\&.\&.\&.\&.3\*(Aq AAGTCCTACATTTAGCCTAGT 5\*(Aq or 5\*(Aq AGGCTATGGGCCTCGCGA 3\*(Aq \&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.|||||| \&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.3\*(Aq AGCGCTCCGGGTATCGGA 5\*(Aq The scoring system is as for the Maximum Complementarity argument\&. In the examples above the scores are 7\&.00 and 6\&.00 respectively\&. Scores are non\-negative, and a score of 0\&.00 indicates that there is no reasonable 3\*(Aq\-anchored global alignment between two oligos\&. In order to estimate 3\*(Aq\-anchored global alignments for candidate primers and primer pairs, Primer assumes that the sequence from which to choose primers is presented 5\*(Aq to 3\*(Aq\&. It is nonsensical to provide a larger value for this parameter than for the Maximum (local) Complementarity parameter because the score of a local alignment will always be at least as great as the score of a global alignment\&. Default value: 3\&.00 .RE .SS "Primer penalty weights" .PP \fB\-maxendstability\fR \fIfloat\fR .RS 4 The maximum stability for the five 3\*(Aq bases of a forward or reverse primer\&. Bigger numbers mean more stable 3\*(Aq ends\&. The value is the maximum delta G for duplex disruption for the five 3\*(Aq bases as calculated using the nearest neighbor parameters published in Breslauer, Frank, Bloecker and Marky, Proc\&. Natl\&. Acad\&. Sci\&. USA, vol 83, pp 3746\-3750\&. EPrimer3 uses a completely permissive default value for backward compatibility (which we may change in the next release)\&. Rychlik recommends a maximum value of 9 (Wojciech Rychlik, \*(AqSelection of Primers for Polymerase Chain Reaction\*(Aq in BA White, Ed\&., \*(AqMethods in Molecular Biology, Vol\&. 15: PCR Protocols: Current Methods and Applications\*(Aq, 1993, pp 31\-40, Humana Press, Totowa NJ)\&. Default value: 9\&.0 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP eprimer3 is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/dottup.1e0000644000000000000000000000570512214054043012531 0ustar '\" t .\" Title: DOTTUP .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DOTTUP" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" dottup \- Displays a wordmatch dotplot of two sequences .SH "SYNOPSIS" .HP \w'\fBdottup\fR\ 'u \fBdottup\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR \fB\-wordsize\ \fR\fB\fIinteger\fR\fR \fB\-stretch\ \fR\fB\fItoggle\fR\fR \fB\-graph\ \fR\fB\fIgraph\fR\fR \fB\-xygraph\ \fR\fB\fIxygraph\fR\fR \fB\-boxit\ \fR\fB\fIboolean\fR\fR .HP \w'\fBdottup\fR\ 'u \fBdottup\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdottup\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Dot plots" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-asequence\fR \fIsequence\fR .RS 4 .RE .PP \fB\-bsequence\fR \fIsequence\fR .RS 4 .RE .SS "Required section" .PP \fB\-wordsize\fR \fIinteger\fR .RS 4 Default value: 10 .RE .SS "Output section" .PP \fB\-stretch\fR \fItoggle\fR .RS 4 Use non\-proportional axes Default value: N .RE .PP \fB\-graph\fR \fIgraph\fR .RS 4 .RE .PP \fB\-xygraph\fR \fIxygraph\fR .RS 4 .RE .PP \fB\-boxit\fR \fIboolean\fR .RS 4 Default value: Y .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP dottup is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/seqretset.1e0000644000000000000000000000506512214054043013230 0ustar '\" t .\" Title: SEQRETSET .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SEQRETSET" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" seqretset \- Reads and writes (returns) a set of sequences all at once .SH "SYNOPSIS" .HP \w'\fBseqretset\fR\ 'u \fBseqretset\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR \fB\-outseq\ \fR\fB\fIseqoutset\fR\fR .HP \w'\fBseqretset\fR\ 'u \fBseqretset\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBseqretset\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-feature\fR \fIboolean\fR .RS 4 .RE .PP \fB\-sequence\fR \fIseqset\fR .RS 4 .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqoutset\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP seqretset is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/cachedbfetch.1e0000644000000000000000000000527212214054043013574 0ustar '\" t .\" Title: CACHEDBFETCH .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "CACHEDBFETCH" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" cachedbfetch \- Generates server cache file for Dbfetch/WSDbfetch data sources .SH "SYNOPSIS" .HP \w'\fBcachedbfetch\fR\ 'u \fBcachedbfetch\fR \fB\-servername\ \fR\fB\fIstring\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] \fB\-cachefile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBcachedbfetch\fR\ 'u \fBcachedbfetch\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBcachedbfetch\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data resources" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-servername\fR \fIstring\fR .RS 4 Default value: dbfetch .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .PP \fB\-cachefile\fR \fIoutfile\fR .RS 4 Default value: server\&.$(servername) .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP cachedbfetch is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/fuzzpro.1e0000644000000000000000000000724712214054043012734 0ustar '\" t .\" Title: FUZZPRO .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "FUZZPRO" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" fuzzpro \- Search for patterns in protein sequences .SH "SYNOPSIS" .HP \w'\fBfuzzpro\fR\ 'u \fBfuzzpro\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-pattern\ \fR\fB\fIpattern\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR .HP \w'\fBfuzzpro\fR\ 'u \fBfuzzpro\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfuzzpro\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Motifs" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-pattern\fR \fIpattern\fR .RS 4 The standard IUPAC one\-letter codes for the amino acids are used\&. The symbol \*(Aqx\*(Aq is used for a position where any amino acid is accepted\&. Ambiguities are indicated by listing the acceptable amino acids for a given position, between square parentheses \*(Aq[ ]\*(Aq\&. For example: [ALT] stands for Ala or Leu or Thr\&. Ambiguities are also indicated by listing between a pair of curly brackets \*(Aq{ }\*(Aq the amino acids that are not accepted at a given position\&. For example: {AM} stands for any amino acid except Ala and Met\&. Each element in a pattern is separated from its neighbor by a \*(Aq\-\*(Aq\&. (Optional in fuzzpro)\&. Repetition of an element of the pattern can be indicated by following that element with a numerical value or a numerical range between parenthesis\&. Examples: x(3) corresponds to x\-x\-x, x(2,4) corresponds to x\-x or x\-x\-x or x\-x\-x\-x\&. When a pattern is restricted to either the N\- or C\-terminal of a sequence, that pattern either starts with a \*(Aq<\*(Aq symbol or respectively ends with a \*(Aq>\*(Aq symbol\&. A period ends the pattern\&. (Optional in fuzzpro)\&. For example, [DE](2)HS{P}X(2)PX(2,4)C .RE .SS "Output section" .PP \fB\-outfile\fR \fIreport\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP fuzzpro is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/seqxrefget.1e0000644000000000000000000000511112214054043013356 0ustar '\" t .\" Title: SEQXREFGET .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SEQXREFGET" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" seqxrefget \- Retrieve all cross\-referenced data for a sequence entry .SH "SYNOPSIS" .HP \w'\fBseqxrefget\fR\ 'u \fBseqxrefget\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBseqxrefget\fR\ 'u \fBseqxrefget\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBseqxrefget\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval:Sequence data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Required section" .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP seqxrefget is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/abiview.1e0000644000000000000000000000651312214054043012636 0ustar '\" t .\" Title: ABIVIEW .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ABIVIEW" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" abiview \- Display the trace in an ABI sequencer file .SH "SYNOPSIS" .HP \w'\fBabiview\fR\ 'u \fBabiview\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR [\fB\-startbase\ \fR\fB\fIinteger\fR\fR] [\fB\-endbase\ \fR\fB\fIinteger\fR\fR] \fB\-separate\ \fR\fB\fIboolean\fR\fR [\fB\-yticks\ \fR\fB\fIboolean\fR\fR] [\fB\-sequence\ \fR\fB\fIboolean\fR\fR] [\fB\-window\ \fR\fB\fIinteger\fR\fR] [\fB\-bases\ \fR\fB\fIstring\fR\fR] .HP \w'\fBabiview\fR\ 'u \fBabiview\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBabiview\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval:Sequence data,Display" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqout\fR .RS 4 .RE .PP \fB\-graph\fR \fIxygraph\fR .RS 4 .RE .PP \fB\-startbase\fR \fIinteger\fR .RS 4 .RE .PP \fB\-endbase\fR \fIinteger\fR .RS 4 Last sequence base to report or display\&. If the default is set to zero then the value of this is taken as the maximum number of bases\&. .RE .PP \fB\-separate\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-yticks\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-sequence\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-window\fR \fIinteger\fR .RS 4 Default value: 40 .RE .PP \fB\-bases\fR \fIstring\fR .RS 4 Default value: GATC .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP abiview is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/wossoutput.1e0000644000000000000000000001605012214054043013461 0ustar '\" t .\" Title: WOSSOUTPUT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "WOSSOUTPUT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" wossoutput \- Finds programs by EDAM output data .SH "SYNOPSIS" .HP \w'\fBwossoutput\fR\ 'u \fBwossoutput\fR \fB\-identifier\ \fR\fB\fIstring\fR\fR [\fB\-explode\ \fR\fB\fIboolean\fR\fR] [\fB\-showkeywords\ \fR\fB\fIboolean\fR\fR] \fB\-sensitive\ \fR\fB\fIboolean\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-emboss\ \fR\fB\fIboolean\fR\fR \fB\-embassy\ \fR\fB\fIboolean\fR\fR \fB\-showembassy\ \fR\fB\fIstring\fR\fR \fB\-colon\ \fR\fB\fIboolean\fR\fR \fB\-gui\ \fR\fB\fIboolean\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fItoggle\fR\fR] [\fB\-groups\ \fR\fB\fIboolean\fR\fR] [\fB\-alphabetic\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBwossoutput\fR\ 'u \fBwossoutput\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBwossoutput\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Documentation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-identifier\fR \fIstring\fR .RS 4 .RE .SS "Additional section" .PP \fB\-explode\fR \fIboolean\fR .RS 4 The groups that EMBOSS applications belong to have two forms, exploded and not exploded\&. The exploded group names are more numerous and often vaguely phrased than the non\-exploded ones\&. The exploded names are formed from definitions of the group names that start like NAME1:NAME2 and which are then expanded into many combinations of the names as: \*(AqNAME1\*(Aq, \*(AqNAME2\*(Aq, \*(AqNAME1 NAME2\*(Aq, NAME2 NAME1\*(Aq\&. The non\-expanded names are simply like: \*(AqNAME1 NAME2\*(Aq\&. Default value: N .RE .PP \fB\-showkeywords\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Advanced section" .PP \fB\-sensitive\fR \fIboolean\fR .RS 4 By default, the query keywords are matched against the EDAM term names (and synonyms) only\&. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches\&. Default value: N .RE .PP \fB\-subclasses\fR \fIboolean\fR .RS 4 Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: Y .RE .PP \fB\-obsolete\fR \fIboolean\fR .RS 4 The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N .RE .PP \fB\-emboss\fR \fIboolean\fR .RS 4 If you use this option then EMBOSS program documentation will be searched\&. If this option is set to be false, then only the EMBASSY programs will be searched (if the \-embassy option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y .RE .PP \fB\-embassy\fR \fIboolean\fR .RS 4 If you use this option then EMBASSY program documentation will be searched\&. If this option is set to be false, then only the EMBOSS programs will be searched (if the \-emboss option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y .RE .PP \fB\-showembassy\fR \fIstring\fR .RS 4 If you use this option then this EMBASSY package program documentation will be searched\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme .RE .PP \fB\-colon\fR \fIboolean\fR .RS 4 The groups that EMBOSS applications belong to up to two levels, for example the primary group \*(AqALIGNMENT\*(Aq has several sub\-groups, or second\-level groups, e\&.g\&.: CONSENSUS, DIFFERENCES, DOT PLOTS, GLOBAL, LOCAL, MULTIPLE\&. To aid programs that parse the output of wossname that require the names of these subgroups, a colon \*(Aq:\*(Aq will be placed between the first and second level of the group name if this option is true\&. Note: This does not apply if the group names have been exploded with the \*(Aqexplode\*(Aq option\&. Default value: N .RE .PP \fB\-gui\fR \fIboolean\fR .RS 4 This option is intended to help those who are designing Graphical User Interfaces to the EMBOSS applications\&. Some EMBOSS programs are inappropriate for running in a GUI, these include other menu programs and interactive editors\&. This option allows you to only report those programs that can be run from a GUI Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .SS "Html section" .PP \fB\-html\fR \fItoggle\fR .RS 4 If you are sending the output to a file, this will format it for displaying as a table in a WWW document\&. Default value: N .RE .PP \fB\-groups\fR \fIboolean\fR .RS 4 If you use this option, then only the group names will be output to the file Default value: N .RE .PP \fB\-alphabetic\fR \fIboolean\fR .RS 4 If you use this option, then you will get a single list of the program names and descriptions instead of the programs being listed in their functional groups\&. Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP wossoutput is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/dbxgcg.1e0000644000000000000000000000672012214054043012446 0ustar '\" t .\" Title: DBXGCG .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DBXGCG" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" dbxgcg \- Index a GCG formatted database using b+tree indices .SH "SYNOPSIS" .HP \w'\fBdbxgcg\fR\ 'u \fBdbxgcg\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-dbresource\ \fR\fB\fIstring\fR\fR \fB\-idformat\ \fR\fB\fIlist\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-filenames\ \fR\fB\fIstring\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-compressed\ \fR\fB\fIboolean\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBdbxgcg\fR\ 'u \fBdbxgcg\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdbxgcg\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-dbname\fR \fIstring\fR .RS 4 .RE .PP \fB\-dbresource\fR \fIstring\fR .RS 4 .RE .PP \fB\-idformat\fR \fIlist\fR .RS 4 Default value: SWISS .RE .PP \fB\-directory\fR \fIdirectory\fR .RS 4 Default value: \&. .RE .PP \fB\-filenames\fR \fIstring\fR .RS 4 Default value: *\&.seq .RE .SS "Required section" .PP \fB\-fields\fR \fIlist\fR .RS 4 Default value: id,acc .RE .PP \fB\-compressed\fR \fIboolean\fR .RS 4 Default value: Y .RE .SS "Advanced section" .PP \fB\-release\fR \fIstring\fR .RS 4 Default value: 0\&.0 .RE .PP \fB\-date\fR \fIstring\fR .RS 4 Default value: 00/00/00 .RE .PP \fB\-exclude\fR \fIstring\fR .RS 4 .RE .SS "Output section" .PP \fB\-indexoutdir\fR \fIoutdir\fR .RS 4 Default value: \&. .RE .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP dbxgcg is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/texttotext.1e0000644000000000000000000000623012214054043013440 0ustar '\" t .\" Title: TEXTTOTEXT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "TEXTTOTEXT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" texttotext \- Convert a plain text format to a different format .SH "SYNOPSIS" .HP \w'\fBtexttotext\fR\ 'u \fBtexttotext\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-type\ \fR\fB\fIlist\fR\fR \fB\-seq\ \fR\fB\fIlist\fR\fR \fB\-feat\ \fR\fB\fIlist\fR\fR \fB\-align\ \fR\fB\fIlist\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBtexttotext\fR\ 'u \fBtexttotext\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBtexttotext\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Misc" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .SS "Required section" .PP \fB\-type\fR \fIlist\fR .RS 4 You must specify the type of file content so that appropriate output format options may be generated\&. .RE .PP \fB\-seq\fR \fIlist\fR .RS 4 This option sets the format of a sequence output file\&. Default value: X .RE .PP \fB\-feat\fR \fIlist\fR .RS 4 This option sets the format of a sequence feature output file\&. Default value: X .RE .PP \fB\-align\fR \fIlist\fR .RS 4 This option sets the format of a sequence alignment output file\&. Default value: X .RE .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP texttotext is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/printsextract.1e0000644000000000000000000000465012214054043014122 0ustar '\" t .\" Title: PRINTSEXTRACT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PRINTSEXTRACT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" printsextract \- Extract data from PRINTS database for use by pscan .SH "SYNOPSIS" .HP \w'\fBprintsextract\fR\ 'u \fBprintsextract\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR .HP \w'\fBprintsextract\fR\ 'u \fBprintsextract\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBprintsextract\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP printsextract is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/seqretsingle.1e0000644000000000000000000000510112214054043013705 0ustar '\" t .\" Title: SEQRETSINGLE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SEQRETSINGLE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" seqretsingle \- Reads and writes (returns) a single sequence .SH "SYNOPSIS" .HP \w'\fBseqretsingle\fR\ 'u \fBseqretsingle\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR .HP \w'\fBseqretsingle\fR\ 'u \fBseqretsingle\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBseqretsingle\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Test" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-feature\fR \fIboolean\fR .RS 4 .RE .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqout\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP seqretsingle is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/notseq.1e0000644000000000000000000000663112214054043012522 0ustar '\" t .\" Title: NOTSEQ .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "NOTSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" notseq \- Write to file a subset of an input stream of sequences .SH "SYNOPSIS" .HP \w'\fBnotseq\fR\ 'u \fBnotseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR [\fB\-junkoutseq\ \fR\fB\fIseqoutall\fR\fR] .HP \w'\fBnotseq\fR\ 'u \fBnotseq\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBnotseq\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Required section" .PP \fB\-exclude\fR \fIstring\fR .RS 4 Enter a list of sequence names or accession numbers to exclude from the sequences read in\&. The excluded sequences will be written to the file specified in the \*(Aqjunkout\*(Aq parameter\&. The remainder will be written out to the file specified in the \*(Aqoutseq\*(Aq parameter\&. The list of sequence names can be separated by either spaces or commas\&. The sequence names can be wildcarded\&. The sequence names are case independent\&. An example of a list of sequences to be excluded is: myseq, hs*, one two three a file containing a list of sequence names can be specified by giving the file name preceeded by a \*(Aq@\*(Aq, eg: \*(Aq@names\&.dat\*(Aq .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .PP \fB\-junkoutseq\fR \fIseqoutall\fR .RS 4 This file collects the sequences which you have excluded from the main output file of sequences\&. Default value: /dev/null .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP notseq is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/dbxuncompress.1e0000644000000000000000000000532112214054043014100 0ustar '\" t .\" Title: DBXUNCOMPRESS .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DBXUNCOMPRESS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" dbxuncompress \- Uncompress a compressed dbx index .SH "SYNOPSIS" .HP \w'\fBdbxuncompress\fR\ 'u \fBdbxuncompress\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-field\ \fR\fB\fIstring\fR\fR \fB\-indexdir\ \fR\fB\fIdirectory\fR\fR \fB\-$(dbname)\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBdbxuncompress\fR\ 'u \fBdbxuncompress\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdbxuncompress\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-dbname\fR \fIstring\fR .RS 4 .RE .PP \fB\-field\fR \fIstring\fR .RS 4 .RE .PP \fB\-indexdir\fR \fIdirectory\fR .RS 4 .RE .SS "Required section" .SS "Advanced section" .SS "Output section" .PP \fB\-$(dbname)\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP dbxuncompress is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/entret.1e0000644000000000000000000000515412214054043012511 0ustar '\" t .\" Title: ENTRET .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ENTRET" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" entret \- Retrieves sequence entries from flatfile databases and files .SH "SYNOPSIS" .HP \w'\fBentret\fR\ 'u \fBentret\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-firstonly\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBentret\fR\ 'u \fBentret\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBentret\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit,Data retrieval:Sequence data,Data retrieval:Text data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Advanced section" .PP \fB\-firstonly\fR \fIboolean\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP entret is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/complex.1e0000644000000000000000000000746112214054043012662 0ustar '\" t .\" Title: COMPLEX .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "COMPLEX" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" complex \- Find the linguistic complexity in nucleotide sequences .SH "SYNOPSIS" .HP \w'\fBcomplex\fR\ 'u \fBcomplex\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-lwin\ \fR\fB\fIinteger\fR\fR \fB\-step\ \fR\fB\fIinteger\fR\fR \fB\-jmin\ \fR\fB\fIinteger\fR\fR \fB\-jmax\ \fR\fB\fIinteger\fR\fR \fB\-omnia\ \fR\fB\fItoggle\fR\fR \fB\-sim\ \fR\fB\fIinteger\fR\fR \fB\-freq\ \fR\fB\fIboolean\fR\fR \fB\-print\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-ujtablefile\ \fR\fB\fIoutfile\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBcomplex\fR\ 'u \fBcomplex\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBcomplex\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Composition" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-lwin\fR \fIinteger\fR .RS 4 Default value: 100 .RE .PP \fB\-step\fR \fIinteger\fR .RS 4 Displacement of the window over the sequence Default value: 5 .RE .PP \fB\-jmin\fR \fIinteger\fR .RS 4 Default value: 4 .RE .PP \fB\-jmax\fR \fIinteger\fR .RS 4 Default value: 6 .RE .SS "Advanced section" .PP \fB\-omnia\fR \fItoggle\fR .RS 4 Calculate over a set of sequences Default value: N .RE .PP \fB\-sim\fR \fIinteger\fR .RS 4 Calculate the linguistic complexity by comparison with a number of simulations having a uniform distribution of bases .RE .PP \fB\-freq\fR \fIboolean\fR .RS 4 Execute the simulation of a sequence based on the base frequency of the original sequence Default value: N .RE .SS "Output section" .PP \fB\-print\fR \fIboolean\fR .RS 4 Generate a file named UjTable containing the values of Uj for each word j in the real sequence(s) and in any simulated sequences Default value: N .RE .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-ujtablefile\fR \fIoutfile\fR .RS 4 Default value: complex\&.ujtable .RE .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP complex is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/trimseq.1e0000644000000000000000000000746012214054043012676 0ustar '\" t .\" Title: TRIMSEQ .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "TRIMSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" trimseq \- Remove unwanted characters from start and end of sequence(s) .SH "SYNOPSIS" .HP \w'\fBtrimseq\fR\ 'u \fBtrimseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-window\ \fR\fB\fIinteger\fR\fR] [\fB\-percent\ \fR\fB\fIfloat\fR\fR] [\fB\-strict\ \fR\fB\fIboolean\fR\fR] [\fB\-star\ \fR\fB\fIboolean\fR\fR] \fB\-left\ \fR\fB\fIboolean\fR\fR \fB\-right\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBtrimseq\fR\ 'u \fBtrimseq\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBtrimseq\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Additional section" .PP \fB\-window\fR \fIinteger\fR .RS 4 This determines the size of the region that is considered when deciding whether the percentage of ambiguity is greater than the threshold\&. A value of 5 means that a region of 5 letters in the sequence is shifted along the sequence from the ends and trimming is done only if there is a greater or equal percentage of ambiguity than the threshold percentage\&. Default value: 1 .RE .PP \fB\-percent\fR \fIfloat\fR .RS 4 This is the threshold of the percentage ambiguity in the window required in order to trim a sequence\&. Default value: 100\&.0 .RE .PP \fB\-strict\fR \fIboolean\fR .RS 4 In nucleic sequences, trim off not only N\*(Aqs and X\*(Aqs, but also the nucleotide IUPAC ambiguity codes M, R, W, S, Y, K, V, H, D and B\&. In protein sequences, trim off not only X\*(Aqs but also B and Z\&. Default value: N .RE .PP \fB\-star\fR \fIboolean\fR .RS 4 In protein sequences, trim off not only X\*(Aqs, but also the *\*(Aqs Default value: N .RE .SS "Advanced section" .PP \fB\-left\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-right\fR \fIboolean\fR .RS 4 Default value: Y .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP trimseq is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/textsearch.1e0000644000000000000000000000752012214054043013361 0ustar '\" t .\" Title: TEXTSEARCH .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "TEXTSEARCH" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" textsearch \- Search the textual description of sequence(s) .SH "SYNOPSIS" .HP \w'\fBtextsearch\fR\ 'u \fBtextsearch\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-pattern\ \fR\fB\fIstring\fR\fR [\fB\-casesensitive\ \fR\fB\fIboolean\fR\fR] [\fB\-html\ \fR\fB\fIboolean\fR\fR] \fB\-only\ \fR\fB\fIboolean\fR\fR \fB\-heading\ \fR\fB\fIboolean\fR\fR \fB\-usa\ \fR\fB\fIboolean\fR\fR \fB\-accession\ \fR\fB\fIboolean\fR\fR \fB\-name\ \fR\fB\fIboolean\fR\fR \fB\-description\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBtextsearch\fR\ 'u \fBtextsearch\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBtextsearch\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval:Text data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Required section" .PP \fB\-pattern\fR \fIstring\fR .RS 4 The search pattern is a regular expression\&. Use a | to indicate OR\&. For example: human|mouse will find text with either \*(Aqhuman\*(Aq OR \*(Aqmouse\*(Aq in the text .RE .SS "Additional section" .PP \fB\-casesensitive\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Output section" .PP \fB\-html\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-only\fR \fIboolean\fR .RS 4 This is a way of shortening the command line if you only want a few things to be displayed\&. Instead of specifying: \*(Aq\-nohead \-noname \-nousa \-noacc \-nodesc\*(Aq to get only the name output, you can specify \*(Aq\-only \-name\*(Aq Default value: N .RE .PP \fB\-heading\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-usa\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-accession\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-name\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-description\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP textsearch is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/seqret.1e0000644000000000000000000000522112214054043012506 0ustar '\" t .\" Title: SEQRET .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SEQRET" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" seqret \- Reads and writes (returns) sequences .SH "SYNOPSIS" .HP \w'\fBseqret\fR\ 'u \fBseqret\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-firstonly\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBseqret\fR\ 'u \fBseqret\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBseqret\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval,Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-feature\fR \fIboolean\fR .RS 4 .RE .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Advanced section" .PP \fB\-firstonly\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP seqret is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/sizeseq.1e0000644000000000000000000000545312214054043012675 0ustar '\" t .\" Title: SIZESEQ .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SIZESEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" sizeseq \- Sort sequences by size .SH "SYNOPSIS" .HP \w'\fBsizeseq\fR\ 'u \fBsizeseq\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR \fB\-descending\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBsizeseq\fR\ 'u \fBsizeseq\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBsizeseq\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-feature\fR \fIboolean\fR .RS 4 Sequence feature information will be retained if this option is set\&. .RE .PP \fB\-sequences\fR \fIseqset\fR .RS 4 .RE .SS "Required section" .PP \fB\-descending\fR \fIboolean\fR .RS 4 By default the shortest sequence is given first\&. Default value: N .RE .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP sizeseq is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/embossdata.1e0000644000000000000000000000651012214054043013327 0ustar '\" t .\" Title: EMBOSSDATA .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "EMBOSSDATA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" embossdata \- Find and retrieve EMBOSS data files .SH "SYNOPSIS" .HP \w'\fBembossdata\fR\ 'u \fBembossdata\fR [\fB\-showall\ \fR\fB\fItoggle\fR\fR] \fB\-fetch\ \fR\fB\fIboolean\fR\fR \fB\-filename\ \fR\fB\fIstring\fR\fR \fB\-reject\ \fR\fB\fIselection\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] .HP \w'\fBembossdata\fR\ 'u \fBembossdata\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBembossdata\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-showall\fR \fItoggle\fR .RS 4 .RE .PP \fB\-fetch\fR \fIboolean\fR .RS 4 .RE .PP \fB\-filename\fR \fIstring\fR .RS 4 This specifies the name of the file that should be fetched into the current directory or searched for in all of the directories that EMBOSS programs search when looking for a data file\&. The name of the file is not altered when it is fetched\&. .RE .SS "Advanced section" .PP \fB\-reject\fR \fIselection\fR .RS 4 This specifies the names of the sub\-directories of the EMBOSS data directory that should be ignored when displaying data directories\&. Default value: 3, 5, 6 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 This specifies the name of the file that the results of a search for a file in the various data directories is written to\&. By default these results are written to the screen (stdout)\&. Default value: stdout .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP embossdata is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/showserver.1e0000644000000000000000000001172412214054043013417 0ustar '\" t .\" Title: SHOWSERVER .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SHOWSERVER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" showserver \- Displays information on configured servers .SH "SYNOPSIS" .HP \w'\fBshowserver\fR\ 'u \fBshowserver\fR [\fB\-server\ \fR\fB\fIstring\fR\fR] [\fB\-showtypes\ \fR\fB\fIlist\fR\fR] [\fB\-html\ \fR\fB\fIboolean\fR\fR] [\fB\-full\ \fR\fB\fIboolean\fR\fR] [\fB\-methods\ \fR\fB\fIboolean\fR\fR] [\fB\-count\ \fR\fB\fIboolean\fR\fR] [\fB\-cachefile\ \fR\fB\fIboolean\fR\fR] [\fB\-url\ \fR\fB\fIboolean\fR\fR] [\fB\-fields\ \fR\fB\fIboolean\fR\fR] [\fB\-defined\ \fR\fB\fIboolean\fR\fR] [\fB\-serverversion\ \fR\fB\fIboolean\fR\fR] [\fB\-sortby\ \fR\fB\fIlist\fR\fR] \fB\-only\ \fR\fB\fItoggle\fR\fR \fB\-heading\ \fR\fB\fIboolean\fR\fR \fB\-scope\ \fR\fB\fIboolean\fR\fR \fB\-type\ \fR\fB\fIboolean\fR\fR \fB\-id\ \fR\fB\fIboolean\fR\fR \fB\-query\ \fR\fB\fIboolean\fR\fR \fB\-all\ \fR\fB\fIboolean\fR\fR \fB\-comment\ \fR\fB\fIboolean\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] .HP \w'\fBshowserver\fR\ 'u \fBshowserver\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBshowserver\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data resources" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-server\fR \fIstring\fR .RS 4 .RE .SS "Additional section" .PP \fB\-showtypes\fR \fIlist\fR .RS 4 Default value: * .RE .PP \fB\-html\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-full\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-methods\fR \fIboolean\fR .RS 4 This displays the access methods that can be used on this server, for all, query or ID access Default value: $(full) .RE .PP \fB\-count\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-cachefile\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-url\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-fields\fR \fIboolean\fR .RS 4 This displays the search fields that can be used on this server, other than the standard \*(Aqid\*(Aq or \*(Aqacc\*(Aq fields\&. Default value: $(full) .RE .PP \fB\-defined\fR \fIboolean\fR .RS 4 This displays a short name for the file containing the server definition Default value: $(full) .RE .PP \fB\-serverversion\fR \fIboolean\fR .RS 4 Default value: $(full) .RE .PP \fB\-sortby\fR \fIlist\fR .RS 4 Default value: type .RE .SS "Advanced section" .PP \fB\-only\fR \fItoggle\fR .RS 4 This is a way of shortening the command line if you only want a few standard columns to be displayed\&. Instead of specifying: \*(Aq\-nohead \-notype \-noid \-noquery \-noall\*(Aq to get only the comment output, you can specify \*(Aq\-only \-comment\*(Aq Default value: N .RE .PP \fB\-heading\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-scope\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-type\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-id\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-query\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-all\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-comment\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP showserver is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/seqrettype.1e0000644000000000000000000000535512214054043013420 0ustar '\" t .\" Title: SEQRETTYPE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SEQRETTYPE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" seqrettype \- Reads and writes (returns) sequences .SH "SYNOPSIS" .HP \w'\fBseqrettype\fR\ 'u \fBseqrettype\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-type\ \fR\fB\fIlist\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-firstonly\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBseqrettype\fR\ 'u \fBseqrettype\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBseqrettype\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-feature\fR \fIboolean\fR .RS 4 .RE .PP \fB\-type\fR \fIlist\fR .RS 4 Default value: any .RE .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Advanced section" .PP \fB\-firstonly\fR \fIboolean\fR .RS 4 .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP seqrettype is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/stretcher.1e0000644000000000000000000000627112214054043013214 0ustar '\" t .\" Title: STRETCHER .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "STRETCHER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" stretcher \- Needleman\-Wunsch rapid global alignment of two sequences .SH "SYNOPSIS" .HP \w'\fBstretcher\fR\ 'u \fBstretcher\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR [\fB\-datafile\ \fR\fB\fImatrix\fR\fR] [\fB\-gapopen\ \fR\fB\fIinteger\fR\fR] [\fB\-gapextend\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIalign\fR\fR .HP \w'\fBstretcher\fR\ 'u \fBstretcher\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBstretcher\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Global" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-asequence\fR \fIsequence\fR .RS 4 .RE .PP \fB\-bsequence\fR \fIsequence\fR .RS 4 .RE .PP \fB\-datafile\fR \fImatrix\fR .RS 4 This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&. .RE .SS "Additional section" .PP \fB\-gapopen\fR \fIinteger\fR .RS 4 Default value: @($(acdprotein)? 12 : 16) .RE .PP \fB\-gapextend\fR \fIinteger\fR .RS 4 Default value: @($(acdprotein)? 2 : 4) .RE .SS "Output section" .PP \fB\-outfile\fR \fIalign\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP stretcher is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/makeprotseq.1e0000644000000000000000000000617412214054043013546 0ustar '\" t .\" Title: MAKEPROTSEQ .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "MAKEPROTSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" makeprotseq \- Create random protein sequences .SH "SYNOPSIS" .HP \w'\fBmakeprotseq\fR\ 'u \fBmakeprotseq\fR \fB\-pepstatsfile\ \fR\fB\fIinfile\fR\fR \fB\-amount\ \fR\fB\fIinteger\fR\fR \fB\-length\ \fR\fB\fIinteger\fR\fR [\fB\-useinsert\ \fR\fB\fItoggle\fR\fR] \fB\-insert\ \fR\fB\fIstring\fR\fR \fB\-start\ \fR\fB\fIinteger\fR\fR \fB\-makeseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBmakeprotseq\fR\ 'u \fBmakeprotseq\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBmakeprotseq\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-pepstatsfile\fR \fIinfile\fR .RS 4 This file should be a pepstats output file\&. Protein sequences will be created with the composition in the pepstats output file\&. .RE .SS "Required section" .PP \fB\-amount\fR \fIinteger\fR .RS 4 Default value: 100 .RE .PP \fB\-length\fR \fIinteger\fR .RS 4 Default value: 100 .RE .PP \fB\-useinsert\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-insert\fR \fIstring\fR .RS 4 String that is inserted into sequence .RE .PP \fB\-start\fR \fIinteger\fR .RS 4 Default value: 1 .RE .SS "Output section" .PP \fB\-makeseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP makeprotseq is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/primers.1e0000644000000000000000000001103212214054043012661 0ustar '\" t .\" Title: PRIMERS .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PRIMERS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" primers \- Simple version of primer3 to pick PCR primers .SH "SYNOPSIS" .HP \w'\fBprimers\fR\ 'u \fBprimers\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-targetregion\ \fR\fB\fIrange\fR\fR] [\fB\-minsize\ \fR\fB\fIinteger\fR\fR] [\fB\-maxsize\ \fR\fB\fIinteger\fR\fR] [\fB\-maxdifftm\ \fR\fB\fIfloat\fR\fR] [\fB\-explainflag\ \fR\fB\fIboolean\fR\fR] [\fB\-numreturn\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBprimers\fR\ 'u \fBprimers\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBprimers\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Primers" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 The sequence from which to choose primers\&. The sequence must be presented 5\*(Aq \-> 3\*(Aq .RE .SS "Additional section" .PP \fB\-targetregion\fR \fIrange\fR .RS 4 If one or more Targets is specified then a legal primer pair must flank at least one of them\&. A Target might be a simple sequence repeat site (for example a CA repeat) or a single\-base\-pair polymorphism\&. The value should be a space\-separated list of , pairs where is the index of the first base of a Target, and is the last E\&.g\&. 50,51 requires primers to surround the 2 bases at positions 50 and 51\&. .RE .PP \fB\-minsize\fR \fIinteger\fR .RS 4 Minimum acceptable length of a primer\&. Must be greater than 0 and less than or equal to MAX\-SIZE\&. Default value: 18 .RE .PP \fB\-maxsize\fR \fIinteger\fR .RS 4 Maximum acceptable length (in bases) of a primer\&. Currently this parameter cannot be larger than 35\&. This limit is governed by the maximum oligo size for which Primer3\*(Aqs melting\-temperature is valid\&. Default value: 27 .RE .PP \fB\-maxdifftm\fR \fIfloat\fR .RS 4 Maximum acceptable (unsigned) difference between the melting temperatures of the forward and reverse primers\&. Default value: 100\&.0 .RE .SS "Output section" .PP \fB\-explainflag\fR \fIboolean\fR .RS 4 If this flag is non\-0, produce LEFT\-EXPLAIN and RIGHT\-EXPLAIN, output, which are intended to provide information on the number of primer pairs that Primer3 examined, and statistics on the number discarded for various reasons\&. Default value: N .RE .PP \fB\-numreturn\fR \fIinteger\fR .RS 4 The maximum number of primer pairs to return\&. Primer pairs returned are sorted by their \*(Aqquality\*(Aq, in other words by the value of the objective function (where a lower number indicates a better primer pair)\&. Caution: setting this parameter to a large value will increase running time\&. Default value: 5 .RE .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP primers is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/marscan.1e0000644000000000000000000000544412214054043012636 0ustar '\" t .\" Title: MARSCAN .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "MARSCAN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" marscan \- Finds matrix/scaffold recognition (MRS) signatures in DNA sequences .SH "SYNOPSIS" .HP \w'\fBmarscan\fR\ 'u \fBmarscan\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR .HP \w'\fBmarscan\fR\ 'u \fBmarscan\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBmarscan\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Gene finding,Nucleic:Functional sites,Nucleic:Transcription" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIreport\fR .RS 4 File for output of MAR/SAR recognition signature (MRS) regions\&. This contains details of the MRS in normal GFF format\&. The MRS consists of two recognition sites, one of 8 bp and one of 16 bp on either sense strand of the genomic DNA, within 200 bp of each other\&. .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP marscan is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/pepnet.1e0000644000000000000000000000642312214054043012503 0ustar '\" t .\" Title: PEPNET .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PEPNET" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" pepnet \- Draw a helical net for a protein sequence .SH "SYNOPSIS" .HP \w'\fBpepnet\fR\ 'u \fBpepnet\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-amphipathic\ \fR\fB\fItoggle\fR\fR \fB\-squares\ \fR\fB\fIstring\fR\fR \fB\-diamonds\ \fR\fB\fIstring\fR\fR \fB\-octags\ \fR\fB\fIstring\fR\fR \fB\-graph\ \fR\fB\fIgraph\fR\fR .HP \w'\fBpepnet\fR\ 'u \fBpepnet\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBpepnet\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Display,Protein:2D Structure" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .SS "Output section" .PP \fB\-amphipathic\fR \fItoggle\fR .RS 4 If this is true then the residues ACFGILMVWY are marked as squares and all other residues are unmarked\&. This overrides any other markup that you may have specified using the qualifiers \*(Aq\-squares\*(Aq, \*(Aq\-diamonds\*(Aq and \*(Aq\-octags\*(Aq\&. .RE .PP \fB\-squares\fR \fIstring\fR .RS 4 By default the aliphatic residues ILVM are marked with squares\&. Default value: ILVM .RE .PP \fB\-diamonds\fR \fIstring\fR .RS 4 By default the residues DENQST are marked with diamonds\&. Default value: DENQST .RE .PP \fB\-octags\fR \fIstring\fR .RS 4 By default the positively charged residues HKR are marked with octagons\&. Default value: HKR .RE .PP \fB\-graph\fR \fIgraph\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP pepnet is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/ontotext.1e0000644000000000000000000000572712214054043013102 0ustar '\" t .\" Title: ONTOTEXT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ONTOTEXT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" ontotext \- Get ontology term(s) original full text .SH "SYNOPSIS" .HP \w'\fBontotext\fR\ 'u \fBontotext\fR \fB\-oboterms\ \fR\fB\fIobo\fR\fR [\fB\-subclasses\ \fR\fB\fIboolean\fR\fR] [\fB\-obsolete\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBontotext\fR\ 'u \fBontotext\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBontotext\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology,Data retrieval:Ontology data,Data retrieval:Text data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-oboterms\fR \fIobo\fR .RS 4 .RE .SS "Additional section" .PP \fB\-subclasses\fR \fIboolean\fR .RS 4 Extend the query matches to include all terms which are specialisations (sub\-classes) of the matched terms\&. Default value: N .RE .PP \fB\-obsolete\fR \fIboolean\fR .RS 4 The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N .RE .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP ontotext is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/ontogetobsolete.1e0000644000000000000000000000543412214054043014425 0ustar '\" t .\" Title: ONTOGETOBSOLETE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ONTOGETOBSOLETE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" ontogetobsolete \- Get ontology ontology terms .SH "SYNOPSIS" .HP \w'\fBontogetobsolete\fR\ 'u \fBontogetobsolete\fR \fB\-oboterms\ \fR\fB\fIobo\fR\fR [\fB\-subclasses\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutobo\fR\fR .HP \w'\fBontogetobsolete\fR\ 'u \fBontogetobsolete\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBontogetobsolete\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology,Data retrieval:Ontology data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-oboterms\fR \fIobo\fR .RS 4 .RE .SS "Additional section" .PP \fB\-subclasses\fR \fIboolean\fR .RS 4 Extend the query matches to include all terms which are specialisations (sub\-classes) of the matched terms\&. Default value: N .RE .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutobo\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP ontogetobsolete is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/prosextract.1e0000644000000000000000000000465612214054043013574 0ustar '\" t .\" Title: PROSEXTRACT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PROSEXTRACT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" prosextract \- Processes the PROSITE motif database for use by patmatmotifs .SH "SYNOPSIS" .HP \w'\fBprosextract\fR\ 'u \fBprosextract\fR \fB\-prositedir\ \fR\fB\fIdirectory\fR\fR .HP \w'\fBprosextract\fR\ 'u \fBprosextract\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBprosextract\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-prositedir\fR \fIdirectory\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP prosextract is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/edamname.1e0000644000000000000000000000617112214054043012757 0ustar '\" t .\" Title: EDAMNAME .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "EDAMNAME" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" edamname \- Find EDAM ontology terms by name .SH "SYNOPSIS" .HP \w'\fBedamname\fR\ 'u \fBedamname\fR \fB\-query\ \fR\fB\fIstring\fR\fR [\fB\-namespace\ \fR\fB\fIlist\fR\fR] \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-edamname\ \fR\fB\fIoutobo\fR\fR .HP \w'\fBedamname\fR\ 'u \fBedamname\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBedamname\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Data retrieval:Ontology data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-query\fR \fIstring\fR .RS 4 .RE .SS "Additional section" .PP \fB\-namespace\fR \fIlist\fR .RS 4 By default all terms are returned\&. Searches can be limited to one or a few namespaces\&. Default value: * .RE .SS "Advanced section" .PP \fB\-subclasses\fR \fIboolean\fR .RS 4 Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: N .RE .PP \fB\-obsolete\fR \fIboolean\fR .RS 4 The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N .RE .SS "Output section" .PP \fB\-edamname\fR \fIoutobo\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP edamname is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/patmattest.1e0000644000000000000000000000507112214054043013374 0ustar '\" t .\" Title: PATMATTEST .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PATMATTEST" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" patmattest \- Test of pattern matching .SH "SYNOPSIS" .HP \w'\fBpatmattest\fR\ 'u \fBpatmattest\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-expression\ \fR\fB\fIstring\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBpatmattest\fR\ 'u \fBpatmattest\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBpatmattest\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Test" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .PP \fB\-expression\fR \fIstring\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP patmattest is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/wossdata.1e0000644000000000000000000001601712214054043013035 0ustar '\" t .\" Title: WOSSDATA .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "WOSSDATA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" wossdata \- Finds programs by EDAM data .SH "SYNOPSIS" .HP \w'\fBwossdata\fR\ 'u \fBwossdata\fR \fB\-identifier\ \fR\fB\fIstring\fR\fR [\fB\-explode\ \fR\fB\fIboolean\fR\fR] [\fB\-showkeywords\ \fR\fB\fIboolean\fR\fR] \fB\-sensitive\ \fR\fB\fIboolean\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-emboss\ \fR\fB\fIboolean\fR\fR \fB\-embassy\ \fR\fB\fIboolean\fR\fR \fB\-showembassy\ \fR\fB\fIstring\fR\fR \fB\-colon\ \fR\fB\fIboolean\fR\fR \fB\-gui\ \fR\fB\fIboolean\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fItoggle\fR\fR] [\fB\-groups\ \fR\fB\fIboolean\fR\fR] [\fB\-alphabetic\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBwossdata\fR\ 'u \fBwossdata\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBwossdata\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Documentation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-identifier\fR \fIstring\fR .RS 4 .RE .SS "Additional section" .PP \fB\-explode\fR \fIboolean\fR .RS 4 The groups that EMBOSS applications belong to have two forms, exploded and not exploded\&. The exploded group names are more numerous and often vaguely phrased than the non\-exploded ones\&. The exploded names are formed from definitions of the group names that start like NAME1:NAME2 and which are then expanded into many combinations of the names as: \*(AqNAME1\*(Aq, \*(AqNAME2\*(Aq, \*(AqNAME1 NAME2\*(Aq, NAME2 NAME1\*(Aq\&. The non\-expanded names are simply like: \*(AqNAME1 NAME2\*(Aq\&. Default value: N .RE .PP \fB\-showkeywords\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Advanced section" .PP \fB\-sensitive\fR \fIboolean\fR .RS 4 By default, the query keywords are matched against the EDAM term names (and synonyms) only\&. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches\&. Default value: N .RE .PP \fB\-subclasses\fR \fIboolean\fR .RS 4 Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: Y .RE .PP \fB\-obsolete\fR \fIboolean\fR .RS 4 The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N .RE .PP \fB\-emboss\fR \fIboolean\fR .RS 4 If you use this option then EMBOSS program documentation will be searched\&. If this option is set to be false, then only the EMBASSY programs will be searched (if the \-embassy option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y .RE .PP \fB\-embassy\fR \fIboolean\fR .RS 4 If you use this option then EMBASSY program documentation will be searched\&. If this option is set to be false, then only the EMBOSS programs will be searched (if the \-emboss option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y .RE .PP \fB\-showembassy\fR \fIstring\fR .RS 4 If you use this option then this EMBASSY package program documentation will be searched\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme .RE .PP \fB\-colon\fR \fIboolean\fR .RS 4 The groups that EMBOSS applications belong to up to two levels, for example the primary group \*(AqALIGNMENT\*(Aq has several sub\-groups, or second\-level groups, e\&.g\&.: CONSENSUS, DIFFERENCES, DOT PLOTS, GLOBAL, LOCAL, MULTIPLE\&. To aid programs that parse the output of wossname that require the names of these subgroups, a colon \*(Aq:\*(Aq will be placed between the first and second level of the group name if this option is true\&. Note: This does not apply if the group names have been exploded with the \*(Aqexplode\*(Aq option\&. Default value: N .RE .PP \fB\-gui\fR \fIboolean\fR .RS 4 This option is intended to help those who are designing Graphical User Interfaces to the EMBOSS applications\&. Some EMBOSS programs are inappropriate for running in a GUI, these include other menu programs and interactive editors\&. This option allows you to only report those programs that can be run from a GUI Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .SS "Html section" .PP \fB\-html\fR \fItoggle\fR .RS 4 If you are sending the output to a file, this will format it for displaying as a table in a WWW document\&. Default value: N .RE .PP \fB\-groups\fR \fIboolean\fR .RS 4 If you use this option, then only the group names will be output to the file Default value: N .RE .PP \fB\-alphabetic\fR \fIboolean\fR .RS 4 If you use this option, then you will get a single list of the program names and descriptions instead of the programs being listed in their functional groups\&. Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP wossdata is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/edamhasoutput.1e0000644000000000000000000000701312214054043014067 0ustar '\" t .\" Title: EDAMHASOUTPUT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "EDAMHASOUTPUT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" edamhasoutput \- Find EDAM ontology terms by has_output relation .SH "SYNOPSIS" .HP \w'\fBedamhasoutput\fR\ 'u \fBedamhasoutput\fR \fB\-identifier\ \fR\fB\fIstring\fR\fR [\fB\-namespace\ \fR\fB\fIlist\fR\fR] \fB\-sensitive\ \fR\fB\fIboolean\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-edamhasoutput\ \fR\fB\fIoutobo\fR\fR .HP \w'\fBedamhasoutput\fR\ 'u \fBedamhasoutput\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBedamhasoutput\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Data retrieval:Ontology data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-identifier\fR \fIstring\fR .RS 4 .RE .SS "Additional section" .PP \fB\-namespace\fR \fIlist\fR .RS 4 By default all terms are returned\&. Searches can be limited to one or a few namespaces\&. Default value: * .RE .SS "Advanced section" .PP \fB\-sensitive\fR \fIboolean\fR .RS 4 By default, the query keywords are matched against the EDAM term names (and synonyms) only\&. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches\&. Default value: N .RE .PP \fB\-subclasses\fR \fIboolean\fR .RS 4 Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: N .RE .PP \fB\-obsolete\fR \fIboolean\fR .RS 4 The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N .RE .SS "Output section" .PP \fB\-edamhasoutput\fR \fIoutobo\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP edamhasoutput is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/showdb.1e0000644000000000000000000001234112214054043012472 0ustar '\" t .\" Title: SHOWDB .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SHOWDB" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" showdb \- Displays information on configured databases .SH "SYNOPSIS" .HP \w'\fBshowdb\fR\ 'u \fBshowdb\fR [\fB\-database\ \fR\fB\fIstring\fR\fR] [\fB\-html\ \fR\fB\fIboolean\fR\fR] [\fB\-protein\ \fR\fB\fIboolean\fR\fR] [\fB\-nucleic\ \fR\fB\fIboolean\fR\fR] [\fB\-sequence\ \fR\fB\fIboolean\fR\fR] [\fB\-feature\ \fR\fB\fIboolean\fR\fR] [\fB\-text\ \fR\fB\fIboolean\fR\fR] [\fB\-taxonomy\ \fR\fB\fIboolean\fR\fR] [\fB\-resource\ \fR\fB\fIboolean\fR\fR] [\fB\-assembly\ \fR\fB\fIboolean\fR\fR] [\fB\-obo\ \fR\fB\fIboolean\fR\fR] [\fB\-full\ \fR\fB\fIboolean\fR\fR] [\fB\-methods\ \fR\fB\fIboolean\fR\fR] [\fB\-fields\ \fR\fB\fIboolean\fR\fR] [\fB\-defined\ \fR\fB\fIboolean\fR\fR] [\fB\-release\ \fR\fB\fIboolean\fR\fR] \fB\-only\ \fR\fB\fItoggle\fR\fR \fB\-heading\ \fR\fB\fIboolean\fR\fR \fB\-type\ \fR\fB\fIboolean\fR\fR \fB\-id\ \fR\fB\fIboolean\fR\fR \fB\-query\ \fR\fB\fIboolean\fR\fR \fB\-all\ \fR\fB\fIboolean\fR\fR \fB\-comment\ \fR\fB\fIboolean\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] .HP \w'\fBshowdb\fR\ 'u \fBshowdb\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBshowdb\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data resources" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-database\fR \fIstring\fR .RS 4 .RE .SS "Additional section" .PP \fB\-html\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-protein\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-nucleic\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-sequence\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-feature\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-text\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-taxonomy\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-resource\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-assembly\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-obo\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-full\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-methods\fR \fIboolean\fR .RS 4 This displays the access methods that can be used on this database, for all, query or ID access Default value: $(full) .RE .PP \fB\-fields\fR \fIboolean\fR .RS 4 This displays the search fields that can be used on this database, other than the standard \*(Aqid\*(Aq or \*(Aqacc\*(Aq fields\&. Default value: $(full) .RE .PP \fB\-defined\fR \fIboolean\fR .RS 4 This displays a short name for the file containing the database definition Default value: $(full) .RE .PP \fB\-release\fR \fIboolean\fR .RS 4 Default value: $(full) .RE .SS "Advanced section" .PP \fB\-only\fR \fItoggle\fR .RS 4 This is a way of shortening the command line if you only want a few standard columns to be displayed\&. Instead of specifying: \*(Aq\-nohead \-notype \-noid \-noquery \-noall\*(Aq to get only the comment output, you can specify \*(Aq\-only \-comment\*(Aq Default value: N .RE .PP \fB\-heading\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-type\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-id\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-query\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-all\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-comment\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP showdb is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/ontoisobsolete.1e0000644000000000000000000000514512214054043014260 0ustar '\" t .\" Title: ONTOISOBSOLETE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ONTOISOBSOLETE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" ontoisobsolete \- Report whether an ontology term id is obsolete .SH "SYNOPSIS" .HP \w'\fBontoisobsolete\fR\ 'u \fBontoisobsolete\fR \fB\-oboterms\ \fR\fB\fIobo\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBontoisobsolete\fR\ 'u \fBontoisobsolete\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBontoisobsolete\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology,Data retrieval:Ontology data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-oboterms\fR \fIobo\fR .RS 4 .RE .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP ontoisobsolete is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/vectorstrip.1e0000644000000000000000000000640512214054043013574 0ustar '\" t .\" Title: VECTORSTRIP .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "VECTORSTRIP" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" vectorstrip \- Removes vectors from the ends of nucleotide sequence(s) .SH "SYNOPSIS" .HP \w'\fBvectorstrip\fR\ 'u \fBvectorstrip\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-readfile\ \fR\fB\fItoggle\fR\fR \fB\-vectorsfile\ \fR\fB\fIinfile\fR\fR \fB\-mismatch\ \fR\fB\fIinteger\fR\fR \fB\-besthits\ \fR\fB\fIboolean\fR\fR \fB\-alinker\ \fR\fB\fIstring\fR\fR \fB\-blinker\ \fR\fB\fIstring\fR\fR [\fB\-allsequences\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBvectorstrip\fR\ 'u \fBvectorstrip\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBvectorstrip\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Vector input options" .PP \fB\-readfile\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-vectorsfile\fR \fIinfile\fR .RS 4 .RE .SS "Required section" .PP \fB\-mismatch\fR \fIinteger\fR .RS 4 Default value: 10 .RE .PP \fB\-besthits\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-alinker\fR \fIstring\fR .RS 4 .RE .PP \fB\-blinker\fR \fIstring\fR .RS 4 .RE .SS "Output section" .PP \fB\-allsequences\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP vectorstrip is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/showdball.1e0000644000000000000000000001134312214054043013164 0ustar '\" t .\" Title: SHOWDBALL .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 07/20/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.3.1 .\" Language: English .\" .TH "SHOWDBALL" "1e" "07/20/2010" "EMBOSS 6.3.1" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" showdball \- Display information on biological databases .SH "SYNOPSIS" .HP \w'\fBshowdball\fR\ 'u \fBshowdball\fR [\fB\-name\ \fR\fB\fIarraystring\fR\fR] \fB\-dbref\ \fR\fB\fIdatafile\fR\fR \fB\-category\ \fR\fB\fIselection\fR\fR \fB\-edam\ \fR\fB\fIselection\fR\fR \fB\-edam\ \fR\fB\fIselection\fR\fR \fB\-display\ \fR\fB\fIselection\fR\fR [\fB\-html\ \fR\fB\fItoggle\fR\fR] [\fB\-category\ \fR\fB\fIstring\fR\fR] [\fB\-all\ \fR\fB\fItoggle\fR\fR] [\fB\-name\ \fR\fB\fIboolean\fR\fR] [\fB\-server\ \fR\fB\fIboolean\fR\fR] [\fB\-desc\ \fR\fB\fIboolean\fR\fR] \fB\-edam\ \fR\fB\fIboolean\fR\fR \fB\-type\ \fR\fB\fIboolean\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] .HP \w'\fBshowdball\fR\ 'u \fBshowdball\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBshowdball\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Display,Information" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-name\fR \fIarraystring\fR .RS 4 Standard names of databases are given in the EMBOSS datafile \*(Aqdbref\&.dat\*(Aq\&. .RE .PP \fB\-dbref\fR \fIdatafile\fR .RS 4 File of database information including identifier, description, type, URL etc\&. Default value: dbref\&.dat .RE .SS "Required section" .PP \fB\-category\fR \fIselection\fR .RS 4 This specifies the SwissProt categories of database to display in the output file Default value: 1 .RE .PP \fB\-edam\fR \fIselection\fR .RS 4 This specifies the SwissProt categories of database to display in the output file Default value: 1 .RE .PP \fB\-edam\fR \fIselection\fR .RS 4 This specifies the SwissProt categories of database to display in the output file Default value: 1 .RE .PP \fB\-display\fR \fIselection\fR .RS 4 The output can include named database(s) only (\*(Aqdatabase\*(Aq option), databases in one or more categories from SwissProt (\*(Aqcategory\*(Aq) or the EDAM ontology (\*(Aqedam\*(Aq), or all known databases (\*(Aqall\*(Aq)\&. Default value: database .RE .SS "Additional section" .PP \fB\-html\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-category\fR \fIstring\fR .RS 4 .RE .PP \fB\-all\fR \fItoggle\fR .RS 4 This will display all available columns\&. It can be combined with \-noCOLNMAE to display all but the named columns e\&.g\&. \*(Aq\-full \-nodesc\*(Aq\&. Default value: N .RE .PP \fB\-name\fR \fIboolean\fR .RS 4 This displays the column of database names Default value: Y .RE .PP \fB\-server\fR \fIboolean\fR .RS 4 This displays the column of URLs of database servers Default value: Y .RE .PP \fB\-desc\fR \fIboolean\fR .RS 4 This displays the column of database short descriptions Default value: Y .RE .SS "Advanced section" .PP \fB\-edam\fR \fIboolean\fR .RS 4 Default value: $(full) .RE .PP \fB\-type\fR \fIboolean\fR .RS 4 Default value: $(full) .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP showdball is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/infoseq.1e0000644000000000000000000001200612214054043012646 0ustar '\" t .\" Title: INFOSEQ .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "INFOSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" infoseq \- Display basic information about sequences .SH "SYNOPSIS" .HP \w'\fBinfoseq\fR\ 'u \fBinfoseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-columns\ \fR\fB\fIboolean\fR\fR \fB\-delimiter\ \fR\fB\fIstring\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fIboolean\fR\fR] \fB\-only\ \fR\fB\fIboolean\fR\fR \fB\-heading\ \fR\fB\fIboolean\fR\fR \fB\-usa\ \fR\fB\fIboolean\fR\fR \fB\-database\ \fR\fB\fIboolean\fR\fR \fB\-name\ \fR\fB\fIboolean\fR\fR \fB\-accession\ \fR\fB\fIboolean\fR\fR \fB\-gi\ \fR\fB\fIboolean\fR\fR \fB\-seqversion\ \fR\fB\fIboolean\fR\fR \fB\-type\ \fR\fB\fIboolean\fR\fR \fB\-length\ \fR\fB\fIboolean\fR\fR \fB\-pgc\ \fR\fB\fIboolean\fR\fR \fB\-organism\ \fR\fB\fIboolean\fR\fR \fB\-description\ \fR\fB\fIboolean\fR\fR .HP \w'\fBinfoseq\fR\ 'u \fBinfoseq\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBinfoseq\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval:Sequence data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Advanced section" .PP \fB\-columns\fR \fIboolean\fR .RS 4 Set this option on (Y) to print the sequence information into neat, aligned columns in the output file\&. Alternatively, leave it unset (N), in which case the information records will be delimited by a character, which you may specify by using the \-delimiter option\&. In other words, if \-columns is set on, the \-delimiter option is overriden\&. Default value: Y .RE .PP \fB\-delimiter\fR \fIstring\fR .RS 4 This string, which is usually a single character only, is used to delimit individual records in the text output file\&. It could be a space character, a tab character, a pipe character or any other character or string\&. Default value: | .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 If you enter the name of a file here then this program will write the sequence details into that file\&. Default value: stdout .RE .PP \fB\-html\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-only\fR \fIboolean\fR .RS 4 This is a way of shortening the command line if you only want a few things to be displayed\&. Instead of specifying: \*(Aq\-nohead \-noname \-noacc \-notype \-nopgc \-nodesc\*(Aq to get only the length output, you can specify \*(Aq\-only \-length\*(Aq Default value: N .RE .PP \fB\-heading\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-usa\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-database\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-name\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-accession\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-gi\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-seqversion\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-type\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-length\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-pgc\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-organism\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-description\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP infoseq is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/needleall.1e0000644000000000000000000001221712214054043013133 0ustar '\" t .\" Title: NEEDLEALL .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "NEEDLEALL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" needleall \- Many\-to\-many pairwise alignments of two sequence sets .SH "SYNOPSIS" .HP \w'\fBneedleall\fR\ 'u \fBneedleall\fR \fB\-asequence\ \fR\fB\fIseqset\fR\fR \fB\-bsequence\ \fR\fB\fIseqall\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] \fB\-gapopen\ \fR\fB\fIfloat\fR\fR \fB\-gapextend\ \fR\fB\fIfloat\fR\fR [\fB\-endweight\ \fR\fB\fIboolean\fR\fR] [\fB\-endopen\ \fR\fB\fIfloat\fR\fR] [\fB\-endextend\ \fR\fB\fIfloat\fR\fR] [\fB\-minscore\ \fR\fB\fIfloat\fR\fR] \fB\-brief\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIalign\fR\fR [\fB\-errorfile\ \fR\fB\fIoutfile\fR\fR] .HP \w'\fBneedleall\fR\ 'u \fBneedleall\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBneedleall\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Global" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-asequence\fR \fIseqset\fR .RS 4 .RE .PP \fB\-bsequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-datafile\fR \fImatrixf\fR .RS 4 This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&. .RE .SS "Required section" .PP \fB\-gapopen\fR \fIfloat\fR .RS 4 The gap open penalty is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: @($(acdprotein)? 10\&.0 : 10\&.0 ) .RE .PP \fB\-gapextend\fR \fIfloat\fR .RS 4 The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps\&. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring\&. Default value: @($(acdprotein)? 0\&.5 : 0\&.5 ) .RE .SS "Additional section" .PP \fB\-endweight\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-endopen\fR \fIfloat\fR .RS 4 The end gap open penalty is the score taken away when an end gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: @($(acdprotein)? 10\&.0 : 10\&.0 ) .RE .PP \fB\-endextend\fR \fIfloat\fR .RS 4 The end gap extension, penalty is added to the end gap penalty for each base or residue in the end gap\&. Default value: @($(acdprotein)? 0\&.5 : 0\&.5 ) .RE .PP \fB\-minscore\fR \fIfloat\fR .RS 4 Minimum alignment score to report an alignment\&. .RE .SS "Output section" .PP \fB\-brief\fR \fIboolean\fR .RS 4 Brief identity and similarity Default value: Y .RE .PP \fB\-outfile\fR \fIalign\fR .RS 4 .RE .PP \fB\-errorfile\fR \fIoutfile\fR .RS 4 Error file to be written to Default value: needleall\&.error .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP needleall is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/servertell.1e0000644000000000000000000000547212214054043013402 0ustar '\" t .\" Title: SERVERTELL .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SERVERTELL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" servertell \- Display information about a public server .SH "SYNOPSIS" .HP \w'\fBservertell\fR\ 'u \fBservertell\fR \fB\-server\ \fR\fB\fIstring\fR\fR [\fB\-full\ \fR\fB\fIboolean\fR\fR] [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] .HP \w'\fBservertell\fR\ 'u \fBservertell\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBservertell\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data resources" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-server\fR \fIstring\fR .RS 4 The name of the database defined locally for use by EMBOSS\&. .RE .SS "Additional section" .PP \fB\-full\fR \fIboolean\fR .RS 4 The default behaviour is to report for relevant databases only basic information from the EMBOSS database definition Default value: N .RE .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP servertell is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/maskambigprot.1e0000644000000000000000000000516112214054043014046 0ustar '\" t .\" Title: MASKAMBIGPROT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "MASKAMBIGPROT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" maskambigprot \- Masks all ambiguity characters in protein sequences with X .SH "SYNOPSIS" .HP \w'\fBmaskambigprot\fR\ 'u \fBmaskambigprot\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBmaskambigprot\fR\ 'u \fBmaskambigprot\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBmaskambigprot\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-feature\fR \fIboolean\fR .RS 4 .RE .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Advanced section" .SS "Output section" .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP maskambigprot is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/cusp.1e0000644000000000000000000000470112214054043012157 0ustar '\" t .\" Title: CUSP .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "CUSP" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" cusp \- Create a codon usage table from nucleotide sequence(s) .SH "SYNOPSIS" .HP \w'\fBcusp\fR\ 'u \fBcusp\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBcusp\fR\ 'u \fBcusp\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBcusp\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Codon usage" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP cusp is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/seqtax.1e0000644000000000000000000000551312214054043012514 0ustar '\" t .\" Title: SEQTAX .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SEQTAX" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" seqtax \- Extract a list of taxonomy ids from a sequence entry .SH "SYNOPSIS" .HP \w'\fBseqtax\fR\ 'u \fBseqtax\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-html\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBseqtax\fR\ 'u \fBseqtax\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBseqtax\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:Taxonomy" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .SS "Required section" .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 This is the file of NCBI taxonomy IDs that were found in the input sequnce entry\&. .RE .SS "Html section" .PP \fB\-html\fR \fIboolean\fR .RS 4 If you are sending the output to a file, this will format it for displaying as a table in a WWW document\&. Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP seqtax is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/pasteseq.1e0000644000000000000000000000540712214054043013036 0ustar '\" t .\" Title: PASTESEQ .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PASTESEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" pasteseq \- Insert one sequence into another .SH "SYNOPSIS" .HP \w'\fBpasteseq\fR\ 'u \fBpasteseq\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR \fB\-pos\ \fR\fB\fIinteger\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR .HP \w'\fBpasteseq\fR\ 'u \fBpasteseq\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBpasteseq\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-asequence\fR \fIsequence\fR .RS 4 .RE .PP \fB\-bsequence\fR \fIsequence\fR .RS 4 .RE .SS "Required section" .PP \fB\-pos\fR \fIinteger\fR .RS 4 The position in the main input sequence to insert after\&. To insert before the start use the position 0\&. Default value: $(asequence\&.end) .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqout\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP pasteseq is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/charge.1e0000644000000000000000000000550112214054043012435 0ustar '\" t .\" Title: CHARGE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "CHARGE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" charge \- Draw a protein charge plot .SH "SYNOPSIS" .HP \w'\fBcharge\fR\ 'u \fBcharge\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-aadata\ \fR\fB\fIdatafile\fR\fR [\fB\-window\ \fR\fB\fIinteger\fR\fR] \fB\-plot\ \fR\fB\fItoggle\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBcharge\fR\ 'u \fBcharge\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBcharge\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Properties" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-seqall\fR \fIseqall\fR .RS 4 .RE .PP \fB\-aadata\fR \fIdatafile\fR .RS 4 Default value: Eamino\&.dat .RE .SS "Additional section" .PP \fB\-window\fR \fIinteger\fR .RS 4 Default value: 5 .RE .SS "Output section" .PP \fB\-plot\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-graph\fR \fIxygraph\fR .RS 4 .RE .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP charge is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/dbxreport.1e0000644000000000000000000000556512214054043013227 0ustar '\" t .\" Title: DBXREPORT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DBXREPORT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" dbxreport \- Validate index and report internals for dbx databases .SH "SYNOPSIS" .HP \w'\fBdbxreport\fR\ 'u \fBdbxreport\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-fields\ \fR\fB\fIstring\fR\fR \fB\-indexdir\ \fR\fB\fIdirectory\fR\fR \fB\-fullreport\ \fR\fB\fIboolean\fR\fR \fB\-$(dbname)\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBdbxreport\fR\ 'u \fBdbxreport\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdbxreport\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-dbname\fR \fIstring\fR .RS 4 .RE .PP \fB\-fields\fR \fIstring\fR .RS 4 A list of index fields separated by spaces or commas\&. Default value: id .RE .PP \fB\-indexdir\fR \fIdirectory\fR .RS 4 .RE .SS "Required section" .SS "Advanced section" .PP \fB\-fullreport\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Output section" .PP \fB\-$(dbname)\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP dbxreport is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/tmap.1e0000644000000000000000000000510612214054043012146 0ustar '\" t .\" Title: TMAP .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "TMAP" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" tmap \- Predict and plot transmembrane segments in protein sequences .SH "SYNOPSIS" .HP \w'\fBtmap\fR\ 'u \fBtmap\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR .HP \w'\fBtmap\fR\ 'u \fBtmap\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBtmap\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Functional sites" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequences\fR \fIseqset\fR .RS 4 File containing a protein sequence alignment .RE .SS "Output section" .PP \fB\-graph\fR \fIxygraph\fR .RS 4 .RE .PP \fB\-outfile\fR \fIreport\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP tmap is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/edamisid.1e0000644000000000000000000000673212214054043012772 0ustar '\" t .\" Title: EDAMISID .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "EDAMISID" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" edamisid \- Find EDAM ontology terms by is_identifier_of relation .SH "SYNOPSIS" .HP \w'\fBedamisid\fR\ 'u \fBedamisid\fR \fB\-identifier\ \fR\fB\fIstring\fR\fR [\fB\-namespace\ \fR\fB\fIlist\fR\fR] \fB\-sensitive\ \fR\fB\fIboolean\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-edamisid\ \fR\fB\fIoutobo\fR\fR .HP \w'\fBedamisid\fR\ 'u \fBedamisid\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBedamisid\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Data retrieval:Ontology data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-identifier\fR \fIstring\fR .RS 4 .RE .SS "Additional section" .PP \fB\-namespace\fR \fIlist\fR .RS 4 By default all terms are returned\&. Searches can be limited to one or a few namespaces\&. Default value: * .RE .SS "Advanced section" .PP \fB\-sensitive\fR \fIboolean\fR .RS 4 By default, the query keywords are matched against the EDAM term names (and synonyms) only\&. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches\&. Default value: N .RE .PP \fB\-subclasses\fR \fIboolean\fR .RS 4 Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: N .RE .PP \fB\-obsolete\fR \fIboolean\fR .RS 4 The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N .RE .SS "Output section" .PP \fB\-edamisid\fR \fIoutobo\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP edamisid is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/docxmlvalid.1e0000644000000000000000000000555412214054043013522 0ustar '\" t .\" Title: DOCXMLVALID .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DOCXMLVALID" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" docxmlvalid \- Check an XML document is well formed and conforms to a schema .SH "SYNOPSIS" .HP \w'\fBdocxmlvalid\fR\ 'u \fBdocxmlvalid\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-schema\ \fR\fB\fIinfile\fR\fR \fB\-validate\ \fR\fB\fIlist\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBdocxmlvalid\fR\ 'u \fBdocxmlvalid\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdocxmlvalid\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Misc" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .PP \fB\-schema\fR \fIinfile\fR .RS 4 .RE .SS "Required section" .PP \fB\-validate\fR \fIlist\fR .RS 4 This option specifies the type (DTD, XSD or Relax\-NG) of the supplied which will be used to validated the supplied XML file\&. Default value: D .RE .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-logfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP docxmlvalid is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/acdlog.1e0000644000000000000000000000443112214054043012436 0ustar '\" t .\" Title: ACDLOG .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ACDLOG" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" acdlog \- Test application ACD file processing and trace data structures .SH "SYNOPSIS" .HP \w'\fBacdlog\fR\ 'u \fBacdlog\fR .HP \w'\fBacdlog\fR\ 'u \fBacdlog\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBacdlog\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Acd,Data retrieval:Tool data" command group(s)\&. .SH "OPTIONS" .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP acdlog is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/coderet.1e0000644000000000000000000000555512214054043012642 0ustar '\" t .\" Title: CODERET .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "CODERET" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" coderet \- Extract CDS, mRNA and translations from feature tables .SH "SYNOPSIS" .HP \w'\fBcoderet\fR\ 'u \fBcoderet\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-cdsoutseq\ \fR\fB\fIseqoutall\fR\fR \fB\-mrnaoutseq\ \fR\fB\fIseqoutall\fR\fR \fB\-translationoutseq\ \fR\fB\fIseqoutall\fR\fR \fB\-restoutseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBcoderet\fR\ 'u \fBcoderet\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBcoderet\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Translation,Data retrieval:Sequence data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-seqall\fR \fIseqall\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-cdsoutseq\fR \fIseqoutall\fR .RS 4 .RE .PP \fB\-mrnaoutseq\fR \fIseqoutall\fR .RS 4 .RE .PP \fB\-translationoutseq\fR \fIseqoutall\fR .RS 4 .RE .PP \fB\-restoutseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP coderet is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/isdbdata.1e0000644000000000000000000000555112214054043012764 0ustar '\" t .\" Title: ISDBDATA .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ISDBDATA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" isdbdata \- Check whether a supplied string is a known data type/identifier name .SH "SYNOPSIS" .HP \w'\fBisdbdata\fR\ 'u \fBisdbdata\fR [\fB\-term\ \fR\fB\fIstring\fR\fR] [\fB\-termout\ \fR\fB\fItoggle\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBisdbdata\fR\ 'u \fBisdbdata\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBisdbdata\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Information" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-term\fR \fIstring\fR .RS 4 .RE .SS "Required section" .SS "Additional section" .PP \fB\-termout\fR \fItoggle\fR .RS 4 This option will write to file the term statement from the EDAM ontology with a name that matches the supplied string\&. Only the EDAM \*(Aqdata\*(Aq branch (data type or identifier) is checked\&. Default value: N .RE .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP isdbdata is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/digest.1e0000644000000000000000000001053012214054043012461 0ustar '\" t .\" Title: DIGEST .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DIGEST" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" digest \- Reports on protein proteolytic enzyme or reagent cleavage sites .SH "SYNOPSIS" .HP \w'\fBdigest\fR\ 'u \fBdigest\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-mwdata\ \fR\fB\fIdatafile\fR\fR \fB\-menu\ \fR\fB\fIlist\fR\fR \fB\-mono\ \fR\fB\fIboolean\fR\fR \fB\-unfavoured\ \fR\fB\fIboolean\fR\fR \fB\-ragging\ \fR\fB\fIboolean\fR\fR \fB\-termini\ \fR\fB\fIlist\fR\fR \fB\-overlap\ \fR\fB\fIboolean\fR\fR \fB\-allpartials\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR .HP \w'\fBdigest\fR\ 'u \fBdigest\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdigest\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Motifs" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-seqall\fR \fIseqall\fR .RS 4 .RE .PP \fB\-mwdata\fR \fIdatafile\fR .RS 4 Molecular weight data for amino acids Default value: Emolwt\&.dat .RE .SS "Required section" .PP \fB\-menu\fR \fIlist\fR .RS 4 Default value: 1 .RE .PP \fB\-mono\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Advanced section" .PP \fB\-unfavoured\fR \fIboolean\fR .RS 4 Trypsin will not normally cut after \*(AqKR\*(Aq if they are followed by any of \*(AqKRIFLP\*(Aq\&. Lys\-C will not normally cut after \*(AqK\*(Aq if it is followed by \*(AqP\*(Aq\&. Arg\-C will not normally cut after \*(AqR\*(Aq if it is followed by \*(AqP\*(Aq\&. V8\-bicarb will not normally cut after \*(AqE\*(Aq if it is followed by any of \*(AqKREP\*(Aq\&. V8\-phosph will not normally cut after \*(AqDE\*(Aq if they are followed by \*(AqP\*(Aq\&. Chymotrypsin will not normally cut after \*(AqFYWLM\*(Aq if they are followed by \*(AqP\*(Aq\&. Specifying unfavoured shows these unfavoured cuts as well as the favoured ones\&. .RE .PP \fB\-ragging\fR \fIboolean\fR .RS 4 Allows semi\-specific and non\-specific digestion\&. This option is particularly useful for generating lists of peptide sequences for protein identification using mass\-spectrometry\&. .RE .PP \fB\-termini\fR \fIlist\fR .RS 4 Default value: 1 .RE .SS "Output section" .PP \fB\-overlap\fR \fIboolean\fR .RS 4 Used for partial digestion\&. Shows all cuts from favoured cut sites plus 1\&.\&.3, 2\&.\&.4, 3\&.\&.5 etc but not (e\&.g\&.) 2\&.\&.5\&. Overlaps are therefore fragments with exactly one potential cut site within it\&. .RE .PP \fB\-allpartials\fR \fIboolean\fR .RS 4 As for overlap but fragments containing more than one potential cut site are included\&. .RE .PP \fB\-outfile\fR \fIreport\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP digest is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/pepwindowall.1e0000644000000000000000000000561012214054043013712 0ustar '\" t .\" Title: PEPWINDOWALL .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PEPWINDOWALL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" pepwindowall \- Draw Kyte\-Doolittle hydropathy plot for a protein alignment .SH "SYNOPSIS" .HP \w'\fBpepwindowall\fR\ 'u \fBpepwindowall\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR [\fB\-datafile\ \fR\fB\fIdatafile\fR\fR] [\fB\-length\ \fR\fB\fIinteger\fR\fR] [\fB\-normalize\ \fR\fB\fIboolean\fR\fR] \fB\-graph\ \fR\fB\fIxygraph\fR\fR .HP \w'\fBpepwindowall\fR\ 'u \fBpepwindowall\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBpepwindowall\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Properties" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequences\fR \fIseqset\fR .RS 4 File containing a sequence alignment .RE .PP \fB\-datafile\fR \fIdatafile\fR .RS 4 Default value: Enakai\&.dat .RE .SS "Additional section" .PP \fB\-length\fR \fIinteger\fR .RS 4 Default value: 19 .RE .PP \fB\-normalize\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Output section" .PP \fB\-graph\fR \fIxygraph\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP pepwindowall is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/entrails.1e0000644000000000000000000000504612214054043013031 0ustar '\" t .\" Title: ENTRAILS .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ENTRAILS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" entrails \- Reports the internal data from the EMBOSS code .SH "SYNOPSIS" .HP \w'\fBentrails\fR\ 'u \fBentrails\fR [\fB\-fullreport\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBentrails\fR\ 'u \fBentrails\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBentrails\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Misc" command group(s)\&. .SH "OPTIONS" .SS "Additional section" .PP \fB\-fullreport\fR \fIboolean\fR .RS 4 By default, only the essential details are reported Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP entrails is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/cutgextract.1e0000644000000000000000000000626112214054043013545 0ustar '\" t .\" Title: CUTGEXTRACT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "CUTGEXTRACT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" cutgextract \- Extract codon usage tables from CUTG database .SH "SYNOPSIS" .HP \w'\fBcutgextract\fR\ 'u \fBcutgextract\fR \fB\-directory\ \fR\fB\fIdirlist\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-wildspec\ \fR\fB\fIstring\fR\fR \fB\-species\ \fR\fB\fIstring\fR\fR \fB\-allrecords\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-filename\ \fR\fB\fIstring\fR\fR .HP \w'\fBcutgextract\fR\ 'u \fBcutgextract\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBcutgextract\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-directory\fR \fIdirlist\fR .RS 4 .RE .SS "Required section" .SS "Advanced section" .PP \fB\-release\fR \fIstring\fR .RS 4 .RE .PP \fB\-wildspec\fR \fIstring\fR .RS 4 Default value: *\&.codon .RE .PP \fB\-species\fR \fIstring\fR .RS 4 Default value: * .RE .PP \fB\-allrecords\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-filename\fR \fIstring\fR .RS 4 Single output filename to override automatic one file for each species\&. Leave blank to generate the filenames\&. Specify a filename to combine several species into one file\&. .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP cutgextract is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/showalign.1e0000644000000000000000000001741012214054043013201 0ustar '\" t .\" Title: SHOWALIGN .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SHOWALIGN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" showalign \- Display a multiple sequence alignment in pretty format .SH "SYNOPSIS" .HP \w'\fBshowalign\fR\ 'u \fBshowalign\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR [\fB\-matrix\ \fR\fB\fImatrix\fR\fR] [\fB\-refseq\ \fR\fB\fIstring\fR\fR] [\fB\-bottom\ \fR\fB\fIboolean\fR\fR] [\fB\-show\ \fR\fB\fIlist\fR\fR] [\fB\-order\ \fR\fB\fIlist\fR\fR] [\fB\-similarcase\ \fR\fB\fIboolean\fR\fR] [\fB\-consensus\ \fR\fB\fIboolean\fR\fR] \fB\-uppercase\ \fR\fB\fIrange\fR\fR \fB\-number\ \fR\fB\fIboolean\fR\fR \fB\-ruler\ \fR\fB\fIboolean\fR\fR \fB\-width\ \fR\fB\fIinteger\fR\fR \fB\-margin\ \fR\fB\fIinteger\fR\fR \fB\-html\ \fR\fB\fIboolean\fR\fR \fB\-highlight\ \fR\fB\fIrange\fR\fR \fB\-plurality\ \fR\fB\fIfloat\fR\fR \fB\-setcase\ \fR\fB\fIfloat\fR\fR \fB\-identity\ \fR\fB\fIfloat\fR\fR \fB\-gaps\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBshowalign\fR\ 'u \fBshowalign\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBshowalign\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Multiple,Data retrieval:Sequence data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqset\fR .RS 4 The sequence alignment to be displayed\&. .RE .PP \fB\-matrix\fR \fImatrix\fR .RS 4 This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&. .RE .SS "Additional section" .PP \fB\-refseq\fR \fIstring\fR .RS 4 If you give the number in the alignment or the name of a sequence, it will be taken to be the reference sequence\&. The reference sequence is always shown in full and is the one against which all the other sequences are compared\&. If this is set to 0 then the consensus sequence will be used as the reference sequence\&. By default the consensus sequence is used as the reference sequence\&. .RE .PP \fB\-bottom\fR \fIboolean\fR .RS 4 If this is true then the reference sequence is displayed at the bottom of the alignment instead of the top\&. Default value: Y .RE .PP \fB\-show\fR \fIlist\fR .RS 4 Default value: N .RE .PP \fB\-order\fR \fIlist\fR .RS 4 Default value: I .RE .PP \fB\-similarcase\fR \fIboolean\fR .RS 4 If this is set True, then when \-show is set to \*(AqSimilarities\*(Aq or \*(AqNon\-identities\*(Aq and a residue is similar but not identical to the reference sequence residue, it will be changed to lower\-case\&. If \-show is set to \*(AqAll\*(Aq then non\-identical, non\-similar residues will be changed to lower\-case\&. If this is False then no change to the case of the residues is made on the basis of their similarity to the reference sequence\&. Default value: Y .RE .PP \fB\-consensus\fR \fIboolean\fR .RS 4 If this is true then the consensus line is displayed\&. Default value: Y .RE .SS "Advanced section" .PP \fB\-uppercase\fR \fIrange\fR .RS 4 Regions to put in uppercase\&. If this is left blank, then the sequence case is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 24\-45, 56\-78 1:45, 67=99;765\&.\&.888 1,5,8,10,23,45,57,99 .RE .PP \fB\-number\fR \fIboolean\fR .RS 4 If this option is true then a line giving the positions in the alignment is displayed every 10 characters above the alignment\&. Default value: Y .RE .PP \fB\-ruler\fR \fIboolean\fR .RS 4 If this option is true then a ruler line marking every 5th and 10th character in the alignment is displayed\&. Default value: Y .RE .PP \fB\-width\fR \fIinteger\fR .RS 4 Default value: 60 .RE .PP \fB\-margin\fR \fIinteger\fR .RS 4 This sets the length of the left\-hand margin for sequence names\&. If the margin is set at 0 then no margin and no names are displayed\&. If the margin is set to a value that is less than the length of a sequence name then the sequence name is displayed truncated to the length of the margin\&. If the margin is set to \-1 then the minimum margin width that will allow all the sequence names to be displayed in full plus a space at the end of the name will automatically be selected\&. Default value: \-1 .RE .PP \fB\-html\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-highlight\fR \fIrange\fR .RS 4 Regions to colour if formatting for HTML\&. If this is left blank, then the sequence is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are followed by any valid HTML font colour\&. Examples of region specifications are: 24\-45 blue 56\-78 orange 1\-100 green 120\-156 red A file of ranges to colour (one range per line) can be specified as \*(Aq@filename\*(Aq\&. .RE .PP \fB\-plurality\fR \fIfloat\fR .RS 4 Set a cut\-off for the % of positive scoring matches below which there is no consensus\&. The default plurality is taken as 50% of the total weight of all the sequences in the alignment\&. Default value: 50\&.0 .RE .PP \fB\-setcase\fR \fIfloat\fR .RS 4 Sets the threshold for the scores of the positive matches above which the consensus is in upper\-case and below which the consensus is in lower\-case\&. By default this is set to be half of the (weight\-adjusted) number of sequences in the alignment\&. Default value: @( $(sequence\&.totweight) / 2) .RE .PP \fB\-identity\fR \fIfloat\fR .RS 4 Provides the facility of setting the required number of identities at a position for it to give a consensus\&. Therefore, if this is set to 100% only columns of identities contribute to the consensus\&. Default value: 0\&.0 .RE .PP \fB\-gaps\fR \fIboolean\fR .RS 4 If this option is true then gap characters can appear in the consensus\&. The alternative is \*(AqN\*(Aq for nucleotide, or \*(AqX\*(Aq for protein Default value: Y .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP showalign is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/finddb.1e0000644000000000000000000000557512214054043012445 0ustar '\" t .\" Title: FINDDB .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.75.2 .\" Date: 07/20/2010 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.3.1 .\" Language: English .\" .TH "FINDDB" "1e" "07/20/2010" "EMBOSS 6.3.1" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" finddb \- Search for a database by keyword .SH "SYNOPSIS" .HP \w'\fBfinddb\fR\ 'u \fBfinddb\fR [\fB\-keyword\ \fR\fB\fIstring\fR\fR] [\fB\-all\ \fR\fB\fItoggle\fR\fR] [\fB\-name\ \fR\fB\fIboolean\fR\fR] [\fB\-server\ \fR\fB\fIboolean\fR\fR] [\fB\-desc\ \fR\fB\fIboolean\fR\fR] [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] .HP \w'\fBfinddb\fR\ 'u \fBfinddb\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfinddb\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Display,Information" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-keyword\fR \fIstring\fR .RS 4 .RE .SS "Additional section" .PP \fB\-all\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-name\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-server\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-desc\fR \fIboolean\fR .RS 4 Default value: Y .RE .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP finddb is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/wordcount.1e0000644000000000000000000000542312214054043013233 0ustar '\" t .\" Title: WORDCOUNT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "WORDCOUNT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" wordcount \- Count and extract unique words in molecular sequence(s) .SH "SYNOPSIS" .HP \w'\fBwordcount\fR\ 'u \fBwordcount\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-wordsize\ \fR\fB\fIinteger\fR\fR [\fB\-mincount\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBwordcount\fR\ 'u \fBwordcount\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBwordcount\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Composition,Protein:Composition" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Required section" .PP \fB\-wordsize\fR \fIinteger\fR .RS 4 Default value: @($(acdprotein)? 2 : 4) .RE .SS "Additional section" .PP \fB\-mincount\fR \fIinteger\fR .RS 4 Default value: 1 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP wordcount is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/extractfeat.1e0000644000000000000000000002462612214054043013527 0ustar '\" t .\" Title: EXTRACTFEAT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "EXTRACTFEAT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" extractfeat \- Extract features from sequence(s) .SH "SYNOPSIS" .HP \w'\fBextractfeat\fR\ 'u \fBextractfeat\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-before\ \fR\fB\fIinteger\fR\fR] [\fB\-after\ \fR\fB\fIinteger\fR\fR] [\fB\-source\ \fR\fB\fIstring\fR\fR] [\fB\-type\ \fR\fB\fIstring\fR\fR] [\fB\-sense\ \fR\fB\fIinteger\fR\fR] [\fB\-minscore\ \fR\fB\fIfloat\fR\fR] [\fB\-maxscore\ \fR\fB\fIfloat\fR\fR] [\fB\-tag\ \fR\fB\fIstring\fR\fR] [\fB\-value\ \fR\fB\fIstring\fR\fR] [\fB\-join\ \fR\fB\fIboolean\fR\fR] [\fB\-featinname\ \fR\fB\fIboolean\fR\fR] [\fB\-describe\ \fR\fB\fIstring\fR\fR] \fB\-outseq\ \fR\fB\fIseqout\fR\fR .HP \w'\fBextractfeat\fR\ 'u \fBextractfeat\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBextractfeat\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit,Feature tables" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Additional section" .PP \fB\-before\fR \fIinteger\fR .RS 4 If this value is greater than 0 then that number of bases or residues before the feature are included in the extracted sequence\&. This allows you to get the context of the feature\&. If this value is negative then the start of the extracted sequence will be this number of bases/residues before the end of the feature\&. So a value of \*(Aq10\*(Aq will start the extraction 10 bases/residues before the start of the sequence, and a value of \*(Aq\-10\*(Aq will start the extraction 10 bases/residues before the end of the feature\&. The output sequence will be padded with \*(AqN\*(Aq or \*(AqX\*(Aq characters if the sequence starts after the required start of the extraction\&. .RE .PP \fB\-after\fR \fIinteger\fR .RS 4 If this value is greater than 0 then that number of bases or residues after the feature are included in the extracted sequence\&. This allows you to get the context of the feature\&. If this value is negative then the end of the extracted sequence will be this number of bases/residues after the start of the feature\&. So a value of \*(Aq10\*(Aq will end the extraction 10 bases/residues after the end of the sequence, and a value of \*(Aq\-10\*(Aq will end the extraction 10 bases/residues after the start of the feature\&. The output sequence will be padded with \*(AqN\*(Aq or \*(AqX\*(Aq characters if the sequence ends before the required end of the extraction\&. .RE .PP \fB\-source\fR \fIstring\fR .RS 4 By default any feature source in the feature table is shown\&. You can set this to match any feature source you wish to show\&. The source name is usually either the name of the program that detected the feature or it is the feature table (eg: EMBL) that the feature came from\&. The source may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one source, separate their names with the character \*(Aq|\*(Aq, eg: gene* | embl Default value: * .RE .PP \fB\-type\fR \fIstring\fR .RS 4 By default every feature in the feature table is extracted\&. You can set this to be any feature type you wish to extract\&. See http://www\&.ebi\&.ac\&.uk/embl/WebFeat/ for a list of the EMBL feature types and see the Uniprot user manual in http://www\&.uniprot\&.org/manual/sequence_annotation for a list of the Uniprot feature types\&. The type may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to extract more than one type, separate their names with the character \*(Aq|\*(Aq, eg: *UTR | intron Default value: * .RE .PP \fB\-sense\fR \fIinteger\fR .RS 4 By default any feature type in the feature table is extracted\&. You can set this to match any feature sense you wish\&. 0 \- any sense, 1 \- forward sense, \-1 \- reverse sense .RE .PP \fB\-minscore\fR \fIfloat\fR .RS 4 Minimum score of feature to extract (see also maxscore) Default value: 0\&.0 .RE .PP \fB\-maxscore\fR \fIfloat\fR .RS 4 Maximum score of feature to extract\&. If both minscore and maxscore are zero (the default), then any score is ignored Default value: 0\&.0 .RE .PP \fB\-tag\fR \fIstring\fR .RS 4 Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \*(AqCDS\*(Aq type of feature may have the tags \*(Aq/codon\*(Aq, \*(Aq/codon_start\*(Aq, \*(Aq/db_xref\*(Aq, \*(Aq/EC_number\*(Aq, \*(Aq/evidence\*(Aq, \*(Aq/exception\*(Aq, \*(Aq/function\*(Aq, \*(Aq/gene\*(Aq, \*(Aq/label\*(Aq, \*(Aq/map\*(Aq, \*(Aq/note\*(Aq, \*(Aq/number\*(Aq, \*(Aq/partial\*(Aq, \*(Aq/product\*(Aq, \*(Aq/protein_id\*(Aq, \*(Aq/pseudo\*(Aq, \*(Aq/standard_name\*(Aq, \*(Aq/translation\*(Aq, \*(Aq/transl_except\*(Aq, \*(Aq/transl_table\*(Aq, or \*(Aq/usedin\*(Aq\&. Some of these tags also have values, for example \*(Aq/gene\*(Aq can have the value of the gene name\&. By default any feature tag in the feature table is extracted\&. You can set this to match any feature tag you wish to show\&. The tag may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to extract more than one tag, separate their names with the character \*(Aq|\*(Aq, eg: gene | label Default value: * .RE .PP \fB\-value\fR \fIstring\fR .RS 4 Tag values are the values associated with a feature tag\&. Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \*(AqCDS\*(Aq type of feature may have the tags \*(Aq/codon\*(Aq, \*(Aq/codon_start\*(Aq, \*(Aq/db_xref\*(Aq, \*(Aq/EC_number\*(Aq, \*(Aq/evidence\*(Aq, \*(Aq/exception\*(Aq, \*(Aq/function\*(Aq, \*(Aq/gene\*(Aq, \*(Aq/label\*(Aq, \*(Aq/map\*(Aq, \*(Aq/note\*(Aq, \*(Aq/number\*(Aq, \*(Aq/partial\*(Aq, \*(Aq/product\*(Aq, \*(Aq/protein_id\*(Aq, \*(Aq/pseudo\*(Aq, \*(Aq/standard_name\*(Aq, \*(Aq/translation\*(Aq, \*(Aq/transl_except\*(Aq, \*(Aq/transl_table\*(Aq, or \*(Aq/usedin\*(Aq\&. Only some of these tags can have values, for example \*(Aq/gene\*(Aq can have the value of the gene name\&. By default any feature tag value in the feature table is shown\&. You can set this to match any feature tag value you wish to show\&. The tag value may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to show more than one tag value, separate their names with a space or the character \*(Aq|\*(Aq, eg: pax* | 10 Default value: * .RE .SS "Output section" .PP \fB\-join\fR \fIboolean\fR .RS 4 Some features, such as CDS (coding sequence) and mRNA are composed of introns concatenated together\&. There may be other forms of \*(Aqjoined\*(Aq sequence, depending on the feature table\&. If this option is set TRUE, then any group of these features will be output as a single sequence\&. If the \*(Aqbefore\*(Aq and \*(Aqafter\*(Aq qualifiers have been set, then only the sequence before the first feature and after the last feature are added\&. Default value: N .RE .PP \fB\-featinname\fR \fIboolean\fR .RS 4 To aid you in identifying the type of feature that has been output, the type of feature is added to the start of the description of the output sequence\&. Sometimes the description of a sequence is lost in subsequent processing of the sequences file, so it is useful for the type to be a part of the sequence ID name\&. If you set this to be TRUE then the name is added to the ID name of the output sequence\&. Default value: N .RE .PP \fB\-describe\fR \fIstring\fR .RS 4 To aid you in identifying some further properties of a feature that has been output, this lets you specify one or more tag names that should be added to the output sequence Description text, together with their values (if any)\&. For example, if this is set to be \*(Aqgene\*(Aq, then if any output feature has the tag (for example) \*(Aq/gene=BRCA1\*(Aq associated with it, then the text \*(Aq(gene=BRCA1)\*(Aq will be added to the Description line\&. Tags are the types of extra values that a feature may have\&. For example in the EMBL feature table, a \*(AqCDS\*(Aq type of feature may have the tags \*(Aq/codon\*(Aq, \*(Aq/codon_start\*(Aq, \*(Aq/db_xref\*(Aq, \*(Aq/EC_number\*(Aq, \*(Aq/evidence\*(Aq, \*(Aq/exception\*(Aq, \*(Aq/function\*(Aq, \*(Aq/gene\*(Aq, \*(Aq/label\*(Aq, \*(Aq/map\*(Aq, \*(Aq/note\*(Aq, \*(Aq/number\*(Aq, \*(Aq/partial\*(Aq, \*(Aq/product\*(Aq, \*(Aq/protein_id\*(Aq, \*(Aq/pseudo\*(Aq, \*(Aq/standard_name\*(Aq, \*(Aq/translation\*(Aq, \*(Aq/transl_except\*(Aq, \*(Aq/transl_table\*(Aq, or \*(Aq/usedin\*(Aq\&. Some of these tags also have values, for example \*(Aq/gene\*(Aq can have the value of the gene name\&. By default no feature tag is displayed\&. You can set this to match any feature tag you wish to show\&. The tag may be wildcarded by using \*(Aq*\*(Aq\&. If you wish to extract more than one tag, separate their names with the character \*(Aq|\*(Aq, eg: gene | label .RE .PP \fB\-outseq\fR \fIseqout\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP extractfeat is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/idtell.1e0000644000000000000000000000520012214054043012455 0ustar '\" t .\" Title: IDTELL .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "IDTELL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" idtell \- Identify the type of a data identifier or query term .SH "SYNOPSIS" .HP \w'\fBidtell\fR\ 'u \fBidtell\fR [\fB\-identifier\ \fR\fB\fIstring\fR\fR] \fB\-dbref\ \fR\fB\fIdatafile\fR\fR .HP \w'\fBidtell\fR\ 'u \fBidtell\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBidtell\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Information" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-identifier\fR \fIstring\fR .RS 4 .RE .PP \fB\-dbref\fR \fIdatafile\fR .RS 4 File of database information including identifier, description, type, URL etc\&. Default value: dbref\&.dat .RE .SS "Required section" .SS "Additional section" .SS "Advanced section" .SS "Output section" .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP idtell is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/showorf.1e0000644000000000000000000000613512214054043012677 0ustar '\" t .\" Title: SHOWORF .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SHOWORF" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" showorf \- Display a nucleotide sequence and translation in pretty format .SH "SYNOPSIS" .HP \w'\fBshoworf\fR\ 'u \fBshoworf\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-frames\ \fR\fB\fIlist\fR\fR [\fB\-table\ \fR\fB\fIlist\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-ruler\ \fR\fB\fIboolean\fR\fR] [\fB\-plabel\ \fR\fB\fIboolean\fR\fR] [\fB\-nlabel\ \fR\fB\fIboolean\fR\fR] \fB\-width\ \fR\fB\fIinteger\fR\fR .HP \w'\fBshoworf\fR\ 'u \fBshoworf\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBshoworf\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Gene finding,Nucleic:Translation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .SS "Required section" .PP \fB\-frames\fR \fIlist\fR .RS 4 Default value: 1,2,3,4,5,6 .RE .SS "Additional section" .PP \fB\-table\fR \fIlist\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-ruler\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-plabel\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-nlabel\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-width\fR \fIinteger\fR .RS 4 Default value: 50 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP showorf is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/isdbname.1e0000644000000000000000000000545212214054043012773 0ustar '\" t .\" Title: ISDBNAME .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ISDBNAME" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" isdbname \- Check whether a supplied string is a known database name .SH "SYNOPSIS" .HP \w'\fBisdbname\fR\ 'u \fBisdbname\fR [\fB\-term\ \fR\fB\fIstring\fR\fR] [\fB\-infout\ \fR\fB\fItoggle\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBisdbname\fR\ 'u \fBisdbname\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBisdbname\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Information" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-term\fR \fIstring\fR .RS 4 .RE .SS "Required section" .SS "Additional section" .PP \fB\-infout\fR \fItoggle\fR .RS 4 This option will write to file information (from the EMBOSS data file DRCAT\&.dat) for the database with a name that matches the supplied string\&. Default value: N .RE .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP isdbname is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/drfindresource.1e0000644000000000000000000000617212214054043014227 0ustar '\" t .\" Title: DRFINDRESOURCE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DRFINDRESOURCE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" drfindresource \- Find public databases by resource .SH "SYNOPSIS" .HP \w'\fBdrfindresource\fR\ 'u \fBdrfindresource\fR \fB\-query\ \fR\fB\fIstring\fR\fR \fB\-sensitive\ \fR\fB\fIboolean\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-drfindresource\ \fR\fB\fIoutresource\fR\fR .HP \w'\fBdrfindresource\fR\ 'u \fBdrfindresource\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdrfindresource\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Data retrieval:Resource data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-query\fR \fIstring\fR .RS 4 .RE .SS "Additional section" .SS "Advanced section" .PP \fB\-sensitive\fR \fIboolean\fR .RS 4 By default, the query keywords are matched against the EDAM term names (and synonyms) only\&. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches\&. Default value: N .RE .PP \fB\-subclasses\fR \fIboolean\fR .RS 4 Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: Y .RE .SS "Output section" .PP \fB\-drfindresource\fR \fIoutresource\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP drfindresource is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/histogramtest.1e0000644000000000000000000000555112214054043014106 0ustar '\" t .\" Title: HISTOGRAMTEST .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "HISTOGRAMTEST" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" histogramtest \- Test of graphics .SH "SYNOPSIS" .HP \w'\fBhistogramtest\fR\ 'u \fBhistogramtest\fR \fB\-sets\ \fR\fB\fIinteger\fR\fR \fB\-points\ \fR\fB\fIinteger\fR\fR \fB\-bins\ \fR\fB\fIinteger\fR\fR \fB\-xstart\ \fR\fB\fIinteger\fR\fR \fB\-xend\ \fR\fB\fIinteger\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR .HP \w'\fBhistogramtest\fR\ 'u \fBhistogramtest\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBhistogramtest\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Test" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sets\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-points\fR \fIinteger\fR .RS 4 Default value: 10 .RE .PP \fB\-bins\fR \fIinteger\fR .RS 4 Default value: $(points) .RE .PP \fB\-xstart\fR \fIinteger\fR .RS 4 .RE .PP \fB\-xend\fR \fIinteger\fR .RS 4 Default value: @($(xstart)+$(points)) .RE .SS "Output section" .PP \fB\-graph\fR \fIxygraph\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP histogramtest is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/wordfinder.1e0000644000000000000000000000761412214054043013356 0ustar '\" t .\" Title: WORDFINDER .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "WORDFINDER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" wordfinder \- Match large sequences against one or more other sequences .SH "SYNOPSIS" .HP \w'\fBwordfinder\fR\ 'u \fBwordfinder\fR \fB\-asequence\ \fR\fB\fIseqset\fR\fR \fB\-bsequence\ \fR\fB\fIseqall\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] \fB\-gapopen\ \fR\fB\fIfloat\fR\fR \fB\-gapextend\ \fR\fB\fIfloat\fR\fR [\fB\-width\ \fR\fB\fIinteger\fR\fR] [\fB\-wordlen\ \fR\fB\fIinteger\fR\fR] [\fB\-limitmatch\ \fR\fB\fIinteger\fR\fR] [\fB\-limitalign\ \fR\fB\fIinteger\fR\fR] [\fB\-lowmatch\ \fR\fB\fIinteger\fR\fR] [\fB\-lowalign\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIalign\fR\fR [\fB\-errorfile\ \fR\fB\fIoutfile\fR\fR] .HP \w'\fBwordfinder\fR\ 'u \fBwordfinder\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBwordfinder\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Local" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-asequence\fR \fIseqset\fR .RS 4 .RE .PP \fB\-bsequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-datafile\fR \fImatrixf\fR .RS 4 This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&. .RE .SS "Required section" .PP \fB\-gapopen\fR \fIfloat\fR .RS 4 Default value: @($(acdprotein)? 30\&.0 : 30\&.0) .RE .PP \fB\-gapextend\fR \fIfloat\fR .RS 4 Default value: @($(acdprotein)? 1\&.5 : 1\&.5) .RE .SS "Additional section" .PP \fB\-width\fR \fIinteger\fR .RS 4 Default value: 16 .RE .PP \fB\-wordlen\fR \fIinteger\fR .RS 4 Default value: 6 .RE .PP \fB\-limitmatch\fR \fIinteger\fR .RS 4 .RE .PP \fB\-limitalign\fR \fIinteger\fR .RS 4 .RE .PP \fB\-lowmatch\fR \fIinteger\fR .RS 4 .RE .PP \fB\-lowalign\fR \fIinteger\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIalign\fR .RS 4 .RE .PP \fB\-errorfile\fR \fIoutfile\fR .RS 4 Error file to be written to Default value: wordfinder\&.error .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP wordfinder is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/cpgplot.1e0000644000000000000000000001074512214054043012662 0ustar '\" t .\" Title: CPGPLOT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "CPGPLOT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" cpgplot \- Identify and plot CpG islands in nucleotide sequence(s) .SH "SYNOPSIS" .HP \w'\fBcpgplot\fR\ 'u \fBcpgplot\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-minlen\ \fR\fB\fIinteger\fR\fR \fB\-minoe\ \fR\fB\fIfloat\fR\fR \fB\-minpc\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-plot\ \fR\fB\fItoggle\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-obsexp\ \fR\fB\fIboolean\fR\fR \fB\-cg\ \fR\fB\fIboolean\fR\fR \fB\-pc\ \fR\fB\fIboolean\fR\fR \fB\-outfeat\ \fR\fB\fIfeatout\fR\fR .HP \w'\fBcpgplot\fR\ 'u \fBcpgplot\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBcpgplot\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:CpG Islands" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Required section" .PP \fB\-window\fR \fIinteger\fR .RS 4 The percentage CG content and the Observed frequency of CG is calculated within a window whose size is set by this parameter\&. The window is moved down the sequence and these statistics are calculated at each position that the window is moved to\&. Default value: 100 .RE .PP \fB\-minlen\fR \fIinteger\fR .RS 4 This sets the minimum length that a CpG island has to be before it is reported\&. Default value: 200 .RE .PP \fB\-minoe\fR \fIfloat\fR .RS 4 This sets the minimum average observed to expected ratio of C plus G to CpG in a set of 10 windows that are required before a CpG island is reported\&. Default value: 0\&.6 .RE .PP \fB\-minpc\fR \fIfloat\fR .RS 4 This sets the minimum average percentage of G plus C a set of 10 windows that are required before a CpG island is reported\&. Default value: 50\&. .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 This sets the name of the file holding the report of the input sequence name, CpG island parameters and the output details of any CpG islands that are found\&. .RE .PP \fB\-plot\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-graph\fR \fIxygraph\fR .RS 4 .RE .PP \fB\-obsexp\fR \fIboolean\fR .RS 4 If this is set to true then the graph of the observed to expected ratio of C plus G to CpG within a window is displayed\&. Default value: Y .RE .PP \fB\-cg\fR \fIboolean\fR .RS 4 If this is set to true then the graph of the regions which have been determined to be CpG islands is displayed\&. Default value: Y .RE .PP \fB\-pc\fR \fIboolean\fR .RS 4 If this is set to true then the graph of the percentage C plus G within a window is displayed\&. Default value: Y .RE .PP \fB\-outfeat\fR \fIfeatout\fR .RS 4 File for output features .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP cpgplot is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/cacheebeyesearch.1e0000644000000000000000000000515212214054043014451 0ustar '\" t .\" Title: CACHEEBEYESEARCH .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "CACHEEBEYESEARCH" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" cacheebeyesearch \- Generates server cache file for EB\-eye search domains .SH "SYNOPSIS" .HP \w'\fBcacheebeyesearch\fR\ 'u \fBcacheebeyesearch\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] \fB\-cachefile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBcacheebeyesearch\fR\ 'u \fBcacheebeyesearch\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBcacheebeyesearch\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data resources" command group(s)\&. .SH "OPTIONS" .SS "Input section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .PP \fB\-cachefile\fR \fIoutfile\fR .RS 4 Default value: server\&.$(servername) .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP cacheebeyesearch is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/noreturn.1e0000644000000000000000000000506712214054043013067 0ustar '\" t .\" Title: NORETURN .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "NORETURN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" noreturn \- Remove carriage return from ASCII files .SH "SYNOPSIS" .HP \w'\fBnoreturn\fR\ 'u \fBnoreturn\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-system\ \fR\fB\fIlist\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBnoreturn\fR\ 'u \fBnoreturn\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBnoreturn\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .SS "Advanced section" .PP \fB\-system\fR \fIlist\fR .RS 4 Default value: unix .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP noreturn is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/density.1e0000644000000000000000000000547412214054043012674 0ustar '\" t .\" Title: DENSITY .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DENSITY" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" density \- Draw a nucleic acid density plot .SH "SYNOPSIS" .HP \w'\fBdensity\fR\ 'u \fBdensity\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR [\fB\-window\ \fR\fB\fIinteger\fR\fR] [\fB\-display\ \fR\fB\fIlist\fR\fR] \fB\-isdual\ \fR\fB\fIvariable\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR .HP \w'\fBdensity\fR\ 'u \fBdensity\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdensity\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Composition" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-seqall\fR \fIseqall\fR .RS 4 .RE .SS "Additional section" .PP \fB\-window\fR \fIinteger\fR .RS 4 Default value: 100 .RE .PP \fB\-display\fR \fIlist\fR .RS 4 Default value: none .RE .SS "Output section" .PP \fB\-isdual\fR \fIvariable\fR .RS 4 .RE .PP \fB\-graph\fR \fIxygraph\fR .RS 4 .RE .PP \fB\-outfile\fR \fIreport\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP density is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/transeq.1e0000644000000000000000000001042712214054043012664 0ustar '\" t .\" Title: TRANSEQ .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "TRANSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" transeq \- Translate nucleic acid sequences .SH "SYNOPSIS" .HP \w'\fBtranseq\fR\ 'u \fBtranseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-frame\ \fR\fB\fIlist\fR\fR] [\fB\-table\ \fR\fB\fIlist\fR\fR] [\fB\-regions\ \fR\fB\fIrange\fR\fR] [\fB\-trim\ \fR\fB\fIboolean\fR\fR] [\fB\-clean\ \fR\fB\fIboolean\fR\fR] \fB\-alternative\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBtranseq\fR\ 'u \fBtranseq\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBtranseq\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Translation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Additional section" .PP \fB\-frame\fR \fIlist\fR .RS 4 Default value: 1 .RE .PP \fB\-table\fR \fIlist\fR .RS 4 .RE .PP \fB\-regions\fR \fIrange\fR .RS 4 Regions to translate\&. If this is left blank, then the complete sequence is translated\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 24\-45, 56\-78 1:45, 67=99;765\&.\&.888 1,5,8,10,23,45,57,99 Note: you should not try to use this option with any other frame than the default, \-frame=1 .RE .PP \fB\-trim\fR \fIboolean\fR .RS 4 This removes all \*(AqX\*(Aq and \*(Aq*\*(Aq characters from the right end of the translation\&. The trimming process starts at the end and continues until the next character is not a \*(AqX\*(Aq or a \*(Aq*\*(Aq Default value: N .RE .PP \fB\-clean\fR \fIboolean\fR .RS 4 This changes all STOP codon positions from the \*(Aq*\*(Aq character to \*(AqX\*(Aq (an unknown residue)\&. This is useful because some programs will not accept protein sequences with \*(Aq*\*(Aq characters in them\&. Default value: N .RE .SS "Advanced section" .PP \fB\-alternative\fR \fIboolean\fR .RS 4 The default definition of frame \*(Aq\-1\*(Aq is the reverse\-complement of the set of codons used in frame 1\&. (Frame \-2 is the set of codons used by frame 2, similarly frames \-3 and 3)\&. This is a common standard, used by the Staden package and other programs\&. If you prefer to define frame \*(Aq\-1\*(Aq as using the set of codons starting with the last codon of the sequence, then set this to be true\&. Default value: N .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP transeq is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/drfindid.1e0000644000000000000000000000607212214054043012773 0ustar '\" t .\" Title: DRFINDID .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DRFINDID" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" drfindid \- Find public databases by identifier .SH "SYNOPSIS" .HP \w'\fBdrfindid\fR\ 'u \fBdrfindid\fR \fB\-query\ \fR\fB\fIstring\fR\fR \fB\-sensitive\ \fR\fB\fIboolean\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-drfindid\ \fR\fB\fIoutresource\fR\fR .HP \w'\fBdrfindid\fR\ 'u \fBdrfindid\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdrfindid\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Data retrieval:Resource data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-query\fR \fIstring\fR .RS 4 .RE .SS "Additional section" .SS "Advanced section" .PP \fB\-sensitive\fR \fIboolean\fR .RS 4 By default, the query keywords are matched against the EDAM term names (and synonyms) only\&. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches\&. Default value: N .RE .PP \fB\-subclasses\fR \fIboolean\fR .RS 4 Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: Y .RE .SS "Output section" .PP \fB\-drfindid\fR \fIoutresource\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP drfindid is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/taxgetdown.1e0000644000000000000000000000503512214054043013372 0ustar '\" t .\" Title: TAXGETDOWN .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "TAXGETDOWN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" taxgetdown \- Get descendants of taxon(s) .SH "SYNOPSIS" .HP \w'\fBtaxgetdown\fR\ 'u \fBtaxgetdown\fR \fB\-taxons\ \fR\fB\fItaxon\fR\fR \fB\-outfile\ \fR\fB\fIouttaxon\fR\fR .HP \w'\fBtaxgetdown\fR\ 'u \fBtaxgetdown\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBtaxgetdown\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:Taxonomy" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-taxons\fR \fItaxon\fR .RS 4 .RE .SS "Required section" .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIouttaxon\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP taxgetdown is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/aligncopypair.1e0000644000000000000000000000571712214054043014056 0ustar '\" t .\" Title: ALIGNCOPYPAIR .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ALIGNCOPYPAIR" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" aligncopypair \- Reads and writes pairs from alignments .SH "SYNOPSIS" .HP \w'\fBaligncopypair\fR\ 'u \fBaligncopypair\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR [\fB\-name\ \fR\fB\fIstring\fR\fR] [\fB\-comment\ \fR\fB\fIstring\fR\fR] [\fB\-append\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIalign\fR\fR .HP \w'\fBaligncopypair\fR\ 'u \fBaligncopypair\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBaligncopypair\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequences\fR \fIseqset\fR .RS 4 File containing a sequence alignment\&. .RE .SS "Required section" .SS "Additional section" .PP \fB\-name\fR \fIstring\fR .RS 4 .RE .PP \fB\-comment\fR \fIstring\fR .RS 4 .RE .PP \fB\-append\fR \fIboolean\fR .RS 4 This allows you to append the name and comments you have given on to the end of the existing alignment header\&. Default value: N .RE .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIalign\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP aligncopypair is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/dbiblast.1e0000644000000000000000000000775612214054043013006 0ustar '\" t .\" Title: DBIBLAST .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DBIBLAST" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" dbiblast \- Index a BLAST database .SH "SYNOPSIS" .HP \w'\fBdbiblast\fR\ 'u \fBdbiblast\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-filenames\ \fR\fB\fIstring\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-seqtype\ \fR\fB\fIlist\fR\fR \fB\-blastversion\ \fR\fB\fIlist\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-sortoptions\ \fR\fB\fIstring\fR\fR \fB\-maxindex\ \fR\fB\fIinteger\fR\fR \fB\-systemsort\ \fR\fB\fIboolean\fR\fR \fB\-cleanup\ \fR\fB\fIboolean\fR\fR \fB\-sourcefile\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR .HP \w'\fBdbiblast\fR\ 'u \fBdbiblast\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdbiblast\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-dbname\fR \fIstring\fR .RS 4 .RE .PP \fB\-directory\fR \fIdirectory\fR .RS 4 Default value: \&. .RE .PP \fB\-filenames\fR \fIstring\fR .RS 4 Default value: $(dbname) .RE .SS "Required section" .PP \fB\-release\fR \fIstring\fR .RS 4 Default value: 0\&.0 .RE .PP \fB\-date\fR \fIstring\fR .RS 4 Default value: 00/00/00 .RE .PP \fB\-seqtype\fR \fIlist\fR .RS 4 Default value: unknown .RE .PP \fB\-blastversion\fR \fIlist\fR .RS 4 Default value: unknown .RE .SS "Advanced section" .PP \fB\-fields\fR \fIlist\fR .RS 4 Default value: acc .RE .PP \fB\-exclude\fR \fIstring\fR .RS 4 .RE .PP \fB\-sortoptions\fR \fIstring\fR .RS 4 Sort options, typically \*(Aq\-T \&.\*(Aq to use current directory for work files and \*(Aq\-k 1,1\*(Aq to force GNU sort to use the first field Default value: \-T \&. \-k 1,1 .RE .PP \fB\-maxindex\fR \fIinteger\fR .RS 4 .RE .PP \fB\-systemsort\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-cleanup\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-sourcefile\fR \fIboolean\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-indexoutdir\fR \fIoutdir\fR .RS 4 Default value: \&. .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP dbiblast is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/acdtable.1e0000644000000000000000000000445612214054043012753 0ustar '\" t .\" Title: ACDTABLE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ACDTABLE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" acdtable \- Generate an HTML table of parameters from an application ACD file .SH "SYNOPSIS" .HP \w'\fBacdtable\fR\ 'u \fBacdtable\fR .HP \w'\fBacdtable\fR\ 'u \fBacdtable\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBacdtable\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Acd,Data retrieval:Tool data" command group(s)\&. .SH "OPTIONS" .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP acdtable is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/ensembltest.1e0000644000000000000000000000603612214054043013535 0ustar '\" t .\" Title: ENSEMBLTEST .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ENSEMBLTEST" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" ensembltest \- Demonstration of the Ensembl API to be\&. .SH "SYNOPSIS" .HP \w'\fBensembltest\fR\ 'u \fBensembltest\fR \fB\-large\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR \fB\-maxnum\ \fR\fB\fIinteger\fR\fR \fB\-exons\ \fR\fB\fIseqoutall\fR\fR \fB\-transcripts\ \fR\fB\fIseqoutall\fR\fR \fB\-translations\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBensembltest\fR\ 'u \fBensembltest\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBensembltest\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Test" command group(s)\&. .SH "OPTIONS" .SS "Input section" .SS "Required section" .SS "Additional section" .PP \fB\-large\fR \fIboolean\fR .RS 4 Set this to \*(AqY\*(Aq to download large test data sets\&. Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .PP \fB\-maxnum\fR \fIinteger\fR .RS 4 Default value: 25 .RE .PP \fB\-exons\fR \fIseqoutall\fR .RS 4 .RE .PP \fB\-transcripts\fR \fIseqoutall\fR .RS 4 .RE .PP \fB\-translations\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP ensembltest is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/dreg.1e0000644000000000000000000000500612214054043012125 0ustar '\" t .\" Title: DREG .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DREG" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" dreg \- Regular expression search of nucleotide sequence(s) .SH "SYNOPSIS" .HP \w'\fBdreg\fR\ 'u \fBdreg\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-pattern\ \fR\fB\fIregexp\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR .HP \w'\fBdreg\fR\ 'u \fBdreg\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdreg\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Motifs" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-pattern\fR \fIregexp\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIreport\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP dreg is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/dbxflat.1e0000644000000000000000000000707512214054043012640 0ustar '\" t .\" Title: DBXFLAT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DBXFLAT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" dbxflat \- Index a flat file database using b+tree indices .SH "SYNOPSIS" .HP \w'\fBdbxflat\fR\ 'u \fBdbxflat\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-dbresource\ \fR\fB\fIstring\fR\fR \fB\-idformat\ \fR\fB\fIlist\fR\fR \fB\-filenames\ \fR\fB\fIstring\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-compressed\ \fR\fB\fIboolean\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-statistics\ \fR\fB\fIboolean\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBdbxflat\fR\ 'u \fBdbxflat\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdbxflat\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-dbname\fR \fIstring\fR .RS 4 .RE .PP \fB\-dbresource\fR \fIstring\fR .RS 4 .RE .PP \fB\-idformat\fR \fIlist\fR .RS 4 Default value: SWISS .RE .PP \fB\-filenames\fR \fIstring\fR .RS 4 Default value: *\&.dat .RE .PP \fB\-directory\fR \fIdirectory\fR .RS 4 Default value: \&. .RE .SS "Required section" .PP \fB\-fields\fR \fIlist\fR .RS 4 Default value: id,acc .RE .PP \fB\-compressed\fR \fIboolean\fR .RS 4 Default value: Y .RE .SS "Advanced section" .PP \fB\-release\fR \fIstring\fR .RS 4 Default value: 0\&.0 .RE .PP \fB\-date\fR \fIstring\fR .RS 4 Default value: 00/00/00 .RE .PP \fB\-exclude\fR \fIstring\fR .RS 4 .RE .PP \fB\-statistics\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Output section" .PP \fB\-indexoutdir\fR \fIoutdir\fR .RS 4 Default value: \&. .RE .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP dbxflat is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/edialign.1e0000644000000000000000000000777712214054043013001 0ustar '\" t .\" Title: EDIALIGN .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "EDIALIGN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" edialign \- Local multiple alignment of sequences .SH "SYNOPSIS" .HP \w'\fBedialign\fR\ 'u \fBedialign\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR \fB\-nucmode\ \fR\fB\fIlist\fR\fR \fB\-revcomp\ \fR\fB\fIboolean\fR\fR [\fB\-overlapw\ \fR\fB\fIselection\fR\fR] [\fB\-linkage\ \fR\fB\fIlist\fR\fR] [\fB\-maxfragl\ \fR\fB\fIinteger\fR\fR] \fB\-fragmat\ \fR\fB\fIboolean\fR\fR \fB\-fragsim\ \fR\fB\fIinteger\fR\fR [\fB\-itscore\ \fR\fB\fIboolean\fR\fR] [\fB\-threshold\ \fR\fB\fIfloat\fR\fR] \fB\-mask\ \fR\fB\fIboolean\fR\fR \fB\-dostars\ \fR\fB\fIboolean\fR\fR \fB\-starnum\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBedialign\fR\ 'u \fBedialign\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBedialign\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Multiple" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequences\fR \fIseqset\fR .RS 4 .RE .SS "Additional section" .PP \fB\-nucmode\fR \fIlist\fR .RS 4 Nucleic acid sequence alignment mode (simple, translated or mixed) Default value: n .RE .PP \fB\-revcomp\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-overlapw\fR \fIselection\fR .RS 4 By default overlap weights are used when Nseq =<35 but you can set this to \*(Aqyes\*(Aq or \*(Aqno\*(Aq Default value: default (when Nseq =< 35) .RE .PP \fB\-linkage\fR \fIlist\fR .RS 4 Clustering method to construct sequence tree (UPGMA, minimum linkage or maximum linkage) Default value: UPGMA .RE .PP \fB\-maxfragl\fR \fIinteger\fR .RS 4 Default value: 40 .RE .PP \fB\-fragmat\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-fragsim\fR \fIinteger\fR .RS 4 Default value: 4 .RE .PP \fB\-itscore\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-threshold\fR \fIfloat\fR .RS 4 Default value: 0\&.0 .RE .SS "Output section" .PP \fB\-mask\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-dostars\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-starnum\fR \fIinteger\fR .RS 4 Default value: 4 .RE .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP edialign is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/recoder.1e0000644000000000000000000000544112214054043012632 0ustar '\" t .\" Title: RECODER .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "RECODER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" recoder \- Find restriction sites to remove (mutate) with no translation change .SH "SYNOPSIS" .HP \w'\fBrecoder\fR\ 'u \fBrecoder\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-enzymes\ \fR\fB\fIstring\fR\fR \fB\-sshow\ \fR\fB\fIboolean\fR\fR \fB\-tshow\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR .HP \w'\fBrecoder\fR\ 'u \fBrecoder\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBrecoder\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Restriction" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .SS "Required section" .PP \fB\-enzymes\fR \fIstring\fR .RS 4 Default value: all .RE .SS "Output section" .PP \fB\-sshow\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-tshow\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-outfile\fR \fIreport\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP recoder is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/ontoget.1e0000644000000000000000000000564012214054043012667 0ustar '\" t .\" Title: ONTOGET .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ONTOGET" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" ontoget \- Get ontology term(s) .SH "SYNOPSIS" .HP \w'\fBontoget\fR\ 'u \fBontoget\fR \fB\-oboterms\ \fR\fB\fIobo\fR\fR [\fB\-subclasses\ \fR\fB\fIboolean\fR\fR] [\fB\-obsolete\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutobo\fR\fR .HP \w'\fBontoget\fR\ 'u \fBontoget\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBontoget\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology,Data retrieval:Ontology data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-oboterms\fR \fIobo\fR .RS 4 .RE .SS "Additional section" .PP \fB\-subclasses\fR \fIboolean\fR .RS 4 Extend the query matches to include all terms which are specialisations (sub\-classes) of the matched terms\&. Default value: N .RE .PP \fB\-obsolete\fR \fIboolean\fR .RS 4 The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N .RE .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutobo\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP ontoget is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/godef.1e0000644000000000000000000000613012214054043012267 0ustar '\" t .\" Title: GODEF .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "GODEF" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" godef \- Find GO ontology terms by definition .SH "SYNOPSIS" .HP \w'\fBgodef\fR\ 'u \fBgodef\fR \fB\-query\ \fR\fB\fIstring\fR\fR [\fB\-namespace\ \fR\fB\fIlist\fR\fR] \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-godef\ \fR\fB\fIoutobo\fR\fR .HP \w'\fBgodef\fR\ 'u \fBgodef\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBgodef\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:GO,Data retrieval:Ontology data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-query\fR \fIstring\fR .RS 4 .RE .SS "Additional section" .PP \fB\-namespace\fR \fIlist\fR .RS 4 By default all terms are returned\&. Searches can be limited to one or a few namespaces\&. Default value: * .RE .SS "Advanced section" .PP \fB\-subclasses\fR \fIboolean\fR .RS 4 Extend the query matches to include all terms which are specialisations (GO sub\-classes) of the matched type\&. Default value: N .RE .PP \fB\-obsolete\fR \fIboolean\fR .RS 4 The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N .RE .SS "Output section" .PP \fB\-godef\fR \fIoutobo\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP godef is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/jaspscan.1e0000644000000000000000000001003112214054043013000 0ustar '\" t .\" Title: JASPSCAN .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "JASPSCAN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" jaspscan \- Scans DNA sequences for transcription factors .SH "SYNOPSIS" .HP \w'\fBjaspscan\fR\ 'u \fBjaspscan\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-menu\ \fR\fB\fIlist\fR\fR \fB\-matrices\ \fR\fB\fIstring\fR\fR \fB\-threshold\ \fR\fB\fIfloat\fR\fR [\fB\-exclude\ \fR\fB\fIstring\fR\fR] [\fB\-both\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIreport\fR\fR .HP \w'\fBjaspscan\fR\ 'u \fBjaspscan\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBjaspscan\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Transcription" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-menu\fR \fIlist\fR .RS 4 Default value: C .RE .PP \fB\-matrices\fR \fIstring\fR .RS 4 The name \*(Aqall\*(Aq reads in all matrix files from the selected JASPAR matrix set\&. You can specify individual matrices by giving their names with commas between then, such as: \*(Aqma0001\&.1,ma0015*\*(Aq\&. The case of the names is not important\&. You can specify a file of matrix names to read in by giving the name of the file holding the matrix names with a \*(Aq@\*(Aq character in front of it, for example, \*(Aq@matrix\&.list\*(Aq\&. Blank lines and lines starting with a hash character or \*(Aq!\*(Aq are ignored and all other lines are concatenated together with a comma character \*(Aq,\*(Aq and then treated as the list of enzymes to search for\&. An example of a file of matrix names is: ! my matrices ma0001\&.1, ma0002\&.1 ! other matrices ma0010\&.1 ma0032* ma0053\&.1 Default value: all .RE .SS "Required section" .PP \fB\-threshold\fR \fIfloat\fR .RS 4 If the matrix score is greater than or equal to this percentage then a hit will be reported Default value: 80\&.0 .RE .SS "Additional section" .PP \fB\-exclude\fR \fIstring\fR .RS 4 The names of any matrices to exclude from the \*(Aqmatrices\*(Aq list\&. Matrices are specified in the same way as for the selection list\&. .RE .PP \fB\-both\fR \fIboolean\fR .RS 4 If set then both the forward and reverse strands are searched Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIreport\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP jaspscan is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/mwcontam.1e0000644000000000000000000000514212214054043013032 0ustar '\" t .\" Title: MWCONTAM .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "MWCONTAM" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" mwcontam \- Find weights common to multiple molecular weights files .SH "SYNOPSIS" .HP \w'\fBmwcontam\fR\ 'u \fBmwcontam\fR \fB\-files\ \fR\fB\fIfilelist\fR\fR \fB\-tolerance\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBmwcontam\fR\ 'u \fBmwcontam\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBmwcontam\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Composition" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-files\fR \fIfilelist\fR .RS 4 .RE .SS "Required section" .PP \fB\-tolerance\fR \fIfloat\fR .RS 4 Default value: 50\&.0 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP mwcontam is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/domtestb.1e0000644000000000000000000000453712214054043013035 0ustar '\" t .\" Title: DOMTESTB .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DOMTESTB" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" domtestb \- Create, manipulate and write out XML .SH "SYNOPSIS" .HP \w'\fBdomtestb\fR\ 'u \fBdomtestb\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBdomtestb\fR\ 'u \fBdomtestb\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdomtestb\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP domtestb is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/seqretall.1e0000644000000000000000000000474612214054043013212 0ustar '\" t .\" Title: SEQRETALL .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SEQRETALL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" seqretall \- Reads and writes (returns) a set of sequences one at a time .SH "SYNOPSIS" .HP \w'\fBseqretall\fR\ 'u \fBseqretall\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBseqretall\fR\ 'u \fBseqretall\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBseqretall\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP seqretall is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/sqltest.1e0000644000000000000000000000455012214054043012706 0ustar '\" t .\" Title: SQLTEST .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SQLTEST" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" sqltest \- Demonstration of SQL server access .SH "SYNOPSIS" .HP \w'\fBsqltest\fR\ 'u \fBsqltest\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBsqltest\fR\ 'u \fBsqltest\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBsqltest\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Test" command group(s)\&. .SH "OPTIONS" .SS "Input section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP sqltest is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/patmatdb.1e0000644000000000000000000000570612214054043013007 0ustar '\" t .\" Title: PATMATDB .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PATMATDB" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" patmatdb \- Searches protein sequences with a sequence motif .SH "SYNOPSIS" .HP \w'\fBpatmatdb\fR\ 'u \fBpatmatdb\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-motif\ \fR\fB\fIstring\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR .HP \w'\fBpatmatdb\fR\ 'u \fBpatmatdb\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBpatmatdb\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Motifs" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Required section" .PP \fB\-motif\fR \fIstring\fR .RS 4 Patterns for patmatdb are based on the format of pattern used in the PROSITE database\&. For example: \*(Aq[DE](2)HS{P}X(2)PX(2,4)C\*(Aq means two Asps or Glus in any order followed by His, Ser, any residue other then Pro, then two of any residue followed by Pro followed by two to four of any residue followed by Cys\&. The search is case\-independent, so \*(AqAAA\*(Aq matches \*(Aqaaa\*(Aq\&. .RE .SS "Output section" .PP \fB\-outfile\fR \fIreport\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP patmatdb is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/yank.1e0000644000000000000000000000502612214054043012150 0ustar '\" t .\" Title: YANK .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "YANK" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" yank \- Add a sequence reference (a full USA) to a list file .SH "SYNOPSIS" .HP \w'\fByank\fR\ 'u \fByank\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-newfile\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fByank\fR\ 'u \fByank\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fByank\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .SS "Output section" .PP \fB\-newfile\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP yank is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/nohtml.1e0000644000000000000000000000501512214054043012505 0ustar '\" t .\" Title: NOHTML .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "NOHTML" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" nohtml \- Remove mark\-up (e\&.g\&. HTML tags) from an ASCII text file .SH "SYNOPSIS" .HP \w'\fBnohtml\fR\ 'u \fBnohtml\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBnohtml\fR\ 'u \fBnohtml\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBnohtml\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .SS "Required section" .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP nohtml is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/cai.1e0000644000000000000000000000500712214054043011741 0ustar '\" t .\" Title: CAI .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "CAI" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" cai \- Calculate codon adaptation index .SH "SYNOPSIS" .HP \w'\fBcai\fR\ 'u \fBcai\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-cfile\ \fR\fB\fIcodon\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBcai\fR\ 'u \fBcai\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBcai\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Codon usage" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-seqall\fR \fIseqall\fR .RS 4 .RE .PP \fB\-cfile\fR \fIcodon\fR .RS 4 Default value: Eyeast_cai\&.cut .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP cai is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/entrailsbook.1e0000644000000000000000000000501512214054043013700 0ustar '\" t .\" Title: ENTRAILSBOOK .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ENTRAILSBOOK" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" entrailsbook \- Reports the internal structures in EMBOSS book format .SH "SYNOPSIS" .HP \w'\fBentrailsbook\fR\ 'u \fBentrailsbook\fR \fB\-tables\ \fR\fB\fIlist\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBentrailsbook\fR\ 'u \fBentrailsbook\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBentrailsbook\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Misc" command group(s)\&. .SH "OPTIONS" .SS "required section" .PP \fB\-tables\fR \fIlist\fR .RS 4 Default value: all .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP entrailsbook is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/sirna.1e0000644000000000000000000001264412214054043012326 0ustar '\" t .\" Title: SIRNA .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SIRNA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" sirna \- Finds siRNA duplexes in mRNA .SH "SYNOPSIS" .HP \w'\fBsirna\fR\ 'u \fBsirna\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-poliii\ \fR\fB\fIboolean\fR\fR] [\fB\-aa\ \fR\fB\fIboolean\fR\fR] [\fB\-tt\ \fR\fB\fIboolean\fR\fR] [\fB\-polybase\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIreport\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR [\fB\-context\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBsirna\fR\ 'u \fBsirna\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBsirna\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Functional sites,Nucleic:2D structure" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Sequence input options" .PP \fB\-poliii\fR \fIboolean\fR .RS 4 This option allows you to select only the 21 base probes that start with a purine and so can be expressed from Pol III expression vectors\&. This is the NARN(17)YNN pattern that has been suggested by Tuschl et al\&. Default value: N .RE .PP \fB\-aa\fR \fIboolean\fR .RS 4 This option allows you to select only those 23 base regions that start with AA\&. If this option is not selected then regions that start with AA will be favoured by giving them a higher score, but regions that do not start with AA will also be reported\&. Default value: N .RE .PP \fB\-tt\fR \fIboolean\fR .RS 4 This option allows you to select only those 23 base regions that end with TT\&. If this option is not selected then regions that end with TT will be favoured by giving them a higher score, but regions that do not end with TT will also be reported\&. Default value: N .RE .PP \fB\-polybase\fR \fIboolean\fR .RS 4 If this option is FALSE then only those 23 base regions that have no repeat of 4 or more of any bases in a row will be reported\&. No regions will ever be reported that have 4 or more G\*(Aqs in a row\&. Default value: Y .RE .SS "Output section" .PP \fB\-outfile\fR \fIreport\fR .RS 4 The output is a table of the forward and reverse parts of the 21 base siRNA duplex\&. Both the forward and reverse sequences are written 5\*(Aq to 3\*(Aq, ready to be ordered\&. The last two bases have been replaced by \*(AqdTdT\*(Aq\&. The starting position of the 23 base region and the %GC content is also given\&. If you wish to see the complete 23 base sequence, then either look at the sequence in the other output file, or use the qualifier \*(Aq\-context\*(Aq which will display the 23 bases of the forward sequence in this report with the first two bases in brackets\&. These first two bases do not form part of the siRNA probe to be ordered\&. .RE .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 This is a file of the sequences of the 23 base regions that the siRNAs are selected from\&. You may use it to do searches of mRNA databases (e\&.g\&. REFSEQ) to confirm that the probes are unique to the gene you wish to use it on\&. .RE .PP \fB\-context\fR \fIboolean\fR .RS 4 The output report file gives the sequences of the 21 base siRNA regions ready to be ordered\&. This does not give you an indication of the 2 bases before the 21 bases\&. It is often interesting to see which of the suggested possible probe regions have an \*(AqAA\*(Aq in front of them (i\&.e\&. it is useful to see which of the 23 base regions start with an \*(AqAA\*(Aq)\&. This option displays the whole 23 bases of the region with the first two bases in brackets, e\&.g\&. \*(Aq(AA)\*(Aq to give you some context for the probe region\&. YOU SHOULD NOT INCLUDE THE TWO BASES IN BRACKETS WHEN YOU PLACE AN ORDER FOR THE PROBES\&. Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP sirna is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/megamerger.1e0000644000000000000000000000647612214054043013333 0ustar '\" t .\" Title: MEGAMERGER .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "MEGAMERGER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" megamerger \- Merge two large overlapping DNA sequences .SH "SYNOPSIS" .HP \w'\fBmegamerger\fR\ 'u \fBmegamerger\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR \fB\-wordsize\ \fR\fB\fIinteger\fR\fR [\fB\-prefer\ \fR\fB\fIboolean\fR\fR] \fB\-outseq\ \fR\fB\fIseqout\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBmegamerger\fR\ 'u \fBmegamerger\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBmegamerger\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Consensus" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-asequence\fR \fIsequence\fR .RS 4 .RE .PP \fB\-bsequence\fR \fIsequence\fR .RS 4 .RE .SS "Required section" .PP \fB\-wordsize\fR \fIinteger\fR .RS 4 Default value: 20 .RE .SS "Additional section" .PP \fB\-prefer\fR \fIboolean\fR .RS 4 When a mismatch between the two sequence is discovered, one or other of the two sequences must be used to create the merged sequence over this mismatch region\&. The default action is to create the merged sequence using the sequence where the mismatch is closest to that sequence\*(Aqs centre\&. If this option is used, then the first sequence (seqa) will always be used in preference to the other sequence when there is a mismatch\&. Default value: N .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqout\fR .RS 4 .RE .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP megamerger is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/diffseq.1e0000644000000000000000000001032512214054043012625 0ustar '\" t .\" Title: DIFFSEQ .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DIFFSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" diffseq \- Compare and report features of two similar sequences .SH "SYNOPSIS" .HP \w'\fBdiffseq\fR\ 'u \fBdiffseq\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR \fB\-wordsize\ \fR\fB\fIinteger\fR\fR [\fB\-globaldifferences\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIreport\fR\fR \fB\-aoutfeat\ \fR\fB\fIfeatout\fR\fR \fB\-boutfeat\ \fR\fB\fIfeatout\fR\fR .HP \w'\fBdiffseq\fR\ 'u \fBdiffseq\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdiffseq\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Differences" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-asequence\fR \fIsequence\fR .RS 4 .RE .PP \fB\-bsequence\fR \fIsequence\fR .RS 4 .RE .SS "Required section" .PP \fB\-wordsize\fR \fIinteger\fR .RS 4 The similar regions between the two sequences are found by creating a hash table of \*(Aqwordsize\*(Aqd subsequences\&. 10 is a reasonable default\&. Making this value larger (20?) may speed up the program slightly, but will mean that any two differences within \*(Aqwordsize\*(Aq of each other will be grouped as a single region of difference\&. This value may be made smaller (4?) to improve the resolution of nearby differences, but the program will go much slower\&. Default value: 10 .RE .SS "Additional section" .PP \fB\-globaldifferences\fR \fIboolean\fR .RS 4 Normally this program will find regions of identity that are the length of the specified word\-size or greater and will then report the regions of difference between these matching regions\&. This works well and is what most people want if they are working with long overlapping nucleic acid sequences\&. You are usually not interested in the non\-overlapping ends of these sequences\&. If you have protein sequences or short RNA sequences however, you will be interested in differences at the very ends \&. It this option is set to be true then the differences at the ends will also be reported\&. Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIreport\fR .RS 4 .RE .PP \fB\-aoutfeat\fR \fIfeatout\fR .RS 4 File for output of first sequence\*(Aqs features Default value: $(asequence\&.name)\&.diffgff .RE .PP \fB\-boutfeat\fR \fIfeatout\fR .RS 4 File for output of second sequence\*(Aqs features Default value: $(bsequence\&.name)\&.diffgff .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP diffseq is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/textget.1e0000644000000000000000000000474412214054043012700 0ustar '\" t .\" Title: TEXTGET .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "TEXTGET" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" textget \- Get text data entries .SH "SYNOPSIS" .HP \w'\fBtextget\fR\ 'u \fBtextget\fR \fB\-text\ \fR\fB\fItext\fR\fR \fB\-outfile\ \fR\fB\fIouttext\fR\fR .HP \w'\fBtextget\fR\ 'u \fBtextget\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBtextget\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval:Text data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-text\fR \fItext\fR .RS 4 .RE .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIouttext\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP textget is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/cpgreport.1e0000644000000000000000000000553112214054043013214 0ustar '\" t .\" Title: CPGREPORT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "CPGREPORT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" cpgreport \- Identify and report CpG\-rich regions in nucleotide sequence(s) .SH "SYNOPSIS" .HP \w'\fBcpgreport\fR\ 'u \fBcpgreport\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-score\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outfeat\ \fR\fB\fIfeatout\fR\fR .HP \w'\fBcpgreport\fR\ 'u \fBcpgreport\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBcpgreport\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:CpG Islands" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Required section" .PP \fB\-score\fR \fIinteger\fR .RS 4 This sets the score for each CG sequence found\&. A value of 17 is more sensitive, but 28 has also been used with some success\&. Default value: 17 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-outfeat\fR \fIfeatout\fR .RS 4 File for output features .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP cpgreport is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/etandem.1e0000644000000000000000000000606512214054043012627 0ustar '\" t .\" Title: ETANDEM .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ETANDEM" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" etandem \- Finds tandem repeats in a nucleotide sequence .SH "SYNOPSIS" .HP \w'\fBetandem\fR\ 'u \fBetandem\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-minrepeat\ \fR\fB\fIinteger\fR\fR \fB\-maxrepeat\ \fR\fB\fIinteger\fR\fR \fB\-threshold\ \fR\fB\fIinteger\fR\fR \fB\-mismatch\ \fR\fB\fIboolean\fR\fR \fB\-uniform\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR \fB\-origfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBetandem\fR\ 'u \fBetandem\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBetandem\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Repeats" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .SS "Required section" .PP \fB\-minrepeat\fR \fIinteger\fR .RS 4 Default value: 10 .RE .PP \fB\-maxrepeat\fR \fIinteger\fR .RS 4 Default value: $(minrepeat) .RE .SS "Advanced section" .PP \fB\-threshold\fR \fIinteger\fR .RS 4 Default value: 20 .RE .PP \fB\-mismatch\fR \fIboolean\fR .RS 4 .RE .PP \fB\-uniform\fR \fIboolean\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIreport\fR .RS 4 .RE .PP \fB\-origfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP etandem is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/dbshowdat.1e0000644000000000000000000001023112214054043013157 0ustar '\" t .\" Title: DBSHOWDAT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DBSHOWDAT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" dbshowdat \- Show possible database queries that return a given data type .SH "SYNOPSIS" .HP \w'\fBdbshowdat\fR\ 'u \fBdbshowdat\fR \fB\-datatype\ \fR\fB\fIstring\fR\fR \fB\-database\ \fR\fB\fIstring\fR\fR \fB\-identifier\ \fR\fB\fIstring\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBdbshowdat\fR\ 'u \fBdbshowdat\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdbshowdat\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Information" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-datatype\fR \fIstring\fR .RS 4 This is the name of a retrievable datatype from the catalogue of public databases in the EMBOSS data file DRCAT\&.dat\&. The names are terms from the \*(Aqdata\*(Aq branch of the EDAM ontology, http://edamontology\&.sourceforge\&.net/\&. If you are unsure of the available retrievable datatypes for a given database, use dbtellquery\&. If you have a datatype name but are not sure its valid, use isdbdata\&. .RE .SS "Required section" .SS "Additional section" .SS "Advanced section" .PP \fB\-database\fR \fIstring\fR .RS 4 This is the name of a database from the catalogue of public databases in the EMBOSS data file DRCAT\&.dat\&. If you are unsure of the available databases use dbfind\&. If you have a database name but are not sure its valid, use isdbname\&. .RE .PP \fB\-identifier\fR \fIstring\fR .RS 4 This is a data identifier (e\&.g\&. a sequence accession number) that is used to specify the data (of type \*(Aqdatatype\*(Aq) to retrieve\&. If you\*(Aqre unsure of the data identifier(s) that are used for a given query (database/datatype) use dbtellquery\&. The types of data identifier are listed under the \*(AqData identifier\*(Aq branch of the EDAM ontology (http://edamontology\&.sourceforge\&.net/)\&. For example values, see the catalogue of public databases in the EMBOSS data file DRCAT\&.dat\&. If you have a data identifier but are unsure of its type, use idtell\&. .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .SS "Html section" .PP \fB\-html\fR \fIboolean\fR .RS 4 If you are sending the output to a file, this will format it for displaying as a table in a WWW document\&. Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP dbshowdat is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/maskambignuc.1e0000644000000000000000000000515312214054043013650 0ustar '\" t .\" Title: MASKAMBIGNUC .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "MASKAMBIGNUC" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" maskambignuc \- Masks all ambiguity characters in nucleotide sequences with N .SH "SYNOPSIS" .HP \w'\fBmaskambignuc\fR\ 'u \fBmaskambignuc\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBmaskambignuc\fR\ 'u \fBmaskambignuc\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBmaskambignuc\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-feature\fR \fIboolean\fR .RS 4 .RE .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Advanced section" .SS "Output section" .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP maskambignuc is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/pepdigest.1e0000644000000000000000000001057012214054043013172 0ustar '\" t .\" Title: PEPDIGEST .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PEPDIGEST" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" pepdigest \- Reports on protein proteolytic enzyme or reagent cleavage sites .SH "SYNOPSIS" .HP \w'\fBpepdigest\fR\ 'u \fBpepdigest\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-mwdata\ \fR\fB\fIdatafile\fR\fR \fB\-menu\ \fR\fB\fIlist\fR\fR \fB\-mono\ \fR\fB\fIboolean\fR\fR \fB\-unfavoured\ \fR\fB\fIboolean\fR\fR \fB\-ragging\ \fR\fB\fIboolean\fR\fR \fB\-termini\ \fR\fB\fIlist\fR\fR \fB\-overlap\ \fR\fB\fIboolean\fR\fR \fB\-allpartials\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR .HP \w'\fBpepdigest\fR\ 'u \fBpepdigest\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBpepdigest\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Composition" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-seqall\fR \fIseqall\fR .RS 4 .RE .PP \fB\-mwdata\fR \fIdatafile\fR .RS 4 Molecular weight data for amino acids Default value: Emolwt\&.dat .RE .SS "Required section" .PP \fB\-menu\fR \fIlist\fR .RS 4 Default value: 1 .RE .PP \fB\-mono\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Advanced section" .PP \fB\-unfavoured\fR \fIboolean\fR .RS 4 Trypsin will not normally cut after \*(AqKR\*(Aq if they are followed by any of \*(AqKRIFLP\*(Aq\&. Lys\-C will not normally cut after \*(AqK\*(Aq if it is followed by \*(AqP\*(Aq\&. Arg\-C will not normally cut after \*(AqR\*(Aq if it is followed by \*(AqP\*(Aq\&. V8\-bicarb will not normally cut after \*(AqE\*(Aq if it is followed by any of \*(AqKREP\*(Aq\&. V8\-phosph will not normally cut after \*(AqDE\*(Aq if they are followed by \*(AqP\*(Aq\&. Chymotrypsin will not normally cut after \*(AqFYWLM\*(Aq if they are followed by \*(AqP\*(Aq\&. Specifying unfavoured shows these unfavoured cuts as well as the favoured ones\&. .RE .PP \fB\-ragging\fR \fIboolean\fR .RS 4 Allows semi\-specific and non\-specific digestion\&. This option is particularly useful for generating lists of peptide sequences for protein identification using mass\-spectrometry\&. .RE .PP \fB\-termini\fR \fIlist\fR .RS 4 Default value: 1 .RE .SS "Output section" .PP \fB\-overlap\fR \fIboolean\fR .RS 4 Used for partial digestion\&. Shows all cuts from favoured cut sites plus 1\&.\&.3, 2\&.\&.4, 3\&.\&.5 etc but not (e\&.g\&.) 2\&.\&.5\&. Overlaps are therefore fragments with exactly one potential cut site within it\&. .RE .PP \fB\-allpartials\fR \fIboolean\fR .RS 4 As for overlap but fragments containing more than one potential cut site are included\&. .RE .PP \fB\-outfile\fR \fIreport\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP pepdigest is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/prima.1e0000644000000000000000000001066512214054043012323 0ustar '\" t .\" Title: PRIMA .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PRIMA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" prima \- Selects primers for PCR and DNA amplification\&. .SH "SYNOPSIS" .HP \w'\fBprima\fR\ 'u \fBprima\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-targetrange\ \fR\fB\fItoggle\fR\fR \fB\-targetstart\ \fR\fB\fIinteger\fR\fR \fB\-targetend\ \fR\fB\fIinteger\fR\fR \fB\-mintmprimer\ \fR\fB\fIfloat\fR\fR \fB\-maxtmprimer\ \fR\fB\fIfloat\fR\fR \fB\-minplen\ \fR\fB\fIinteger\fR\fR \fB\-maxplen\ \fR\fB\fIinteger\fR\fR \fB\-minpgccont\ \fR\fB\fIfloat\fR\fR \fB\-maxpgccont\ \fR\fB\fIfloat\fR\fR [\fB\-primer\ \fR\fB\fItoggle\fR\fR] \fB\-minprimerlen\ \fR\fB\fIinteger\fR\fR \fB\-maxprimerlen\ \fR\fB\fIinteger\fR\fR \fB\-minpmgccont\ \fR\fB\fIfloat\fR\fR \fB\-maxpmgccont\ \fR\fB\fIfloat\fR\fR \fB\-overlap\ \fR\fB\fIinteger\fR\fR \fB\-saltconc\ \fR\fB\fIfloat\fR\fR \fB\-dnaconc\ \fR\fB\fIfloat\fR\fR \fB\-list\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBprima\fR\ 'u \fBprima\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBprima\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Primers" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .SS "Required section" .SS "Target options" .PP \fB\-targetrange\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-targetstart\fR \fIinteger\fR .RS 4 Default value: $(sequence\&.begin) .RE .PP \fB\-targetend\fR \fIinteger\fR .RS 4 Default value: $(sequence\&.length) .RE .PP \fB\-mintmprimer\fR \fIfloat\fR .RS 4 Default value: 53 .RE .PP \fB\-maxtmprimer\fR \fIfloat\fR .RS 4 Default value: 58 .RE .SS "Additional section" .SS "Product options" .PP \fB\-minplen\fR \fIinteger\fR .RS 4 Default value: 100 .RE .PP \fB\-maxplen\fR \fIinteger\fR .RS 4 Default value: 300 .RE .PP \fB\-minpgccont\fR \fIfloat\fR .RS 4 Default value: \&.40 .RE .PP \fB\-maxpgccont\fR \fIfloat\fR .RS 4 Default value: \&.55 .RE .SS "Primer options" .PP \fB\-primer\fR \fItoggle\fR .RS 4 Specify primer properties Default value: Y .RE .PP \fB\-minprimerlen\fR \fIinteger\fR .RS 4 Default value: 18 .RE .PP \fB\-maxprimerlen\fR \fIinteger\fR .RS 4 Default value: 22 .RE .PP \fB\-minpmgccont\fR \fIfloat\fR .RS 4 Default value: \&.40 .RE .PP \fB\-maxpmgccont\fR \fIfloat\fR .RS 4 Default value: \&.55 .RE .SS "Advanced section" .PP \fB\-overlap\fR \fIinteger\fR .RS 4 Default value: 50 .RE .PP \fB\-saltconc\fR \fIfloat\fR .RS 4 Default value: 50 .RE .PP \fB\-dnaconc\fR \fIfloat\fR .RS 4 Default value: 50 .RE .PP \fB\-list\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP prima is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/martdatasets.1e0000644000000000000000000000551312214054043013703 0ustar '\" t .\" Title: MARTDATASETS .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "MARTDATASETS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" martdatasets \- Return datasets from a mart from a registry .SH "SYNOPSIS" .HP \w'\fBmartdatasets\fR\ 'u \fBmartdatasets\fR \fB\-mart\ \fR\fB\fIstring\fR\fR \fB\-host\ \fR\fB\fIstring\fR\fR \fB\-path\ \fR\fB\fIstring\fR\fR \fB\-port\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBmartdatasets\fR\ 'u \fBmartdatasets\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBmartdatasets\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-mart\fR \fIstring\fR .RS 4 Default value: ensembl .RE .SS "Advanced section" .PP \fB\-host\fR \fIstring\fR .RS 4 Default value: www\&.biomart\&.org .RE .PP \fB\-path\fR \fIstring\fR .RS 4 Default value: /biomart/martservice .RE .PP \fB\-port\fR \fIinteger\fR .RS 4 Default value: 80 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP martdatasets is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/ontogetsibs.1e0000644000000000000000000000540412214054043013546 0ustar '\" t .\" Title: ONTOGETSIBS .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ONTOGETSIBS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" ontogetsibs \- Get ontology term(s) by id with common parent .SH "SYNOPSIS" .HP \w'\fBontogetsibs\fR\ 'u \fBontogetsibs\fR \fB\-oboterms\ \fR\fB\fIobo\fR\fR [\fB\-obsolete\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutobo\fR\fR .HP \w'\fBontogetsibs\fR\ 'u \fBontogetsibs\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBontogetsibs\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology,Data retrieval:Ontology data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-oboterms\fR \fIobo\fR .RS 4 .RE .SS "Additional section" .PP \fB\-obsolete\fR \fIboolean\fR .RS 4 The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N .RE .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutobo\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP ontogetsibs is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/ontogetup.1e0000644000000000000000000000535012214054043013232 0ustar '\" t .\" Title: ONTOGETUP .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ONTOGETUP" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" ontogetup \- Get ontology term(s) by id of child .SH "SYNOPSIS" .HP \w'\fBontogetup\fR\ 'u \fBontogetup\fR \fB\-oboterms\ \fR\fB\fIobo\fR\fR [\fB\-obsolete\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutobo\fR\fR .HP \w'\fBontogetup\fR\ 'u \fBontogetup\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBontogetup\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology,Data retrieval:Ontology data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-oboterms\fR \fIobo\fR .RS 4 .RE .SS "Additional section" .PP \fB\-obsolete\fR \fIboolean\fR .RS 4 The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N .RE .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutobo\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP ontogetup is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/seqxref.1e0000644000000000000000000000506212214054043012663 0ustar '\" t .\" Title: SEQXREF .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SEQXREF" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" seqxref \- Retrieve all database cross\-references for a sequence entry .SH "SYNOPSIS" .HP \w'\fBseqxref\fR\ 'u \fBseqxref\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBseqxref\fR\ 'u \fBseqxref\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBseqxref\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval:Sequence data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Required section" .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP seqxref is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/infobase.1e0000644000000000000000000000521212214054043012771 0ustar '\" t .\" Title: INFOBASE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "INFOBASE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" infobase \- Return information on a given nucleotide base .SH "SYNOPSIS" .HP \w'\fBinfobase\fR\ 'u \fBinfobase\fR \fB\-code\ \fR\fB\fIstring\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBinfobase\fR\ 'u \fBinfobase\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBinfobase\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval:Chemistry data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-code\fR \fIstring\fR .RS 4 Enter IUPAC nucleotide base codes, e\&.g\&. A, C, G, T, R, Y etc\&. Default value: ABCDGHKMNRSTUVWXY .RE .SS "Required section" .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP infobase is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/newcoils.1e0000644000000000000000000000615412214054043013034 0ustar '\" t .\" Title: NEWCOILS .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "NEWCOILS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" newcoils \- Predicts coils protein secondary structure .SH "SYNOPSIS" .HP \w'\fBnewcoils\fR\ 'u \fBnewcoils\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-datafile\ \fR\fB\fIdatafile\fR\fR \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-weighted\ \fR\fB\fIinteger\fR\fR \fB\-verb\ \fR\fB\fIinteger\fR\fR \fB\-mode\ \fR\fB\fIinteger\fR\fR \fB\-minseg\ \fR\fB\fIinteger\fR\fR \fB\-minp\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBnewcoils\fR\ 'u \fBnewcoils\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBnewcoils\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:2D Structure" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-datafile\fR \fIdatafile\fR .RS 4 Default value: Enewcoils\&.mat .RE .SS "Required section" .PP \fB\-window\fR \fIinteger\fR .RS 4 Default value: 21 .RE .PP \fB\-weighted\fR \fIinteger\fR .RS 4 .RE .PP \fB\-verb\fR \fIinteger\fR .RS 4 .RE .PP \fB\-mode\fR \fIinteger\fR .RS 4 .RE .PP \fB\-minseg\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-minp\fR \fIfloat\fR .RS 4 Default value: 0\&.50 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP newcoils is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/taxseq.1e0000644000000000000000000000521212214054043012510 0ustar '\" t .\" Title: TAXSEQ .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "TAXSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" taxseq \- Identify sequence entries containing taxonomy IDs .SH "SYNOPSIS" .HP \w'\fBtaxseq\fR\ 'u \fBtaxseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-ids\ \fR\fB\fIstring\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBtaxseq\fR\ 'u \fBtaxseq\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBtaxseq\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-ids\fR \fIstring\fR .RS 4 .RE .SS "Required section" .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 The list of sequence names will be written to this list file .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP taxseq is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/cons.1e0000644000000000000000000000747312214054043012160 0ustar '\" t .\" Title: CONS .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "CONS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" cons \- Create a consensus sequence from a multiple alignment .SH "SYNOPSIS" .HP \w'\fBcons\fR\ 'u \fBcons\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR [\fB\-datafile\ \fR\fB\fImatrix\fR\fR] [\fB\-plurality\ \fR\fB\fIfloat\fR\fR] [\fB\-identity\ \fR\fB\fIinteger\fR\fR] [\fB\-setcase\ \fR\fB\fIfloat\fR\fR] \fB\-outseq\ \fR\fB\fIseqout\fR\fR [\fB\-name\ \fR\fB\fIstring\fR\fR] .HP \w'\fBcons\fR\ 'u \fBcons\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBcons\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Consensus" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqset\fR .RS 4 File containing a sequence alignment\&. .RE .PP \fB\-datafile\fR \fImatrix\fR .RS 4 This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&. .RE .SS "Additional section" .PP \fB\-plurality\fR \fIfloat\fR .RS 4 Set a cut\-off for the number of positive matches below which there is no consensus\&. The default plurality is taken as half the total weight of all the sequences in the alignment\&. Default value: @( $(sequence\&.totweight) / 2) .RE .PP \fB\-identity\fR \fIinteger\fR .RS 4 Provides the facility of setting the required number of identities at a site for it to give a consensus at that position\&. Therefore, if this is set to the number of sequences in the alignment only columns of identities contribute to the consensus\&. .RE .PP \fB\-setcase\fR \fIfloat\fR .RS 4 Sets the threshold for the positive matches above which the consensus is is upper\-case and below which the consensus is in lower\-case\&. Default value: @( $(sequence\&.totweight) / 2) .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqout\fR .RS 4 .RE .PP \fB\-name\fR \fIstring\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP cons is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/oddcomp.1e0000644000000000000000000000721112214054043012631 0ustar '\" t .\" Title: ODDCOMP .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ODDCOMP" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" oddcomp \- Identify proteins with specified sequence word composition .SH "SYNOPSIS" .HP \w'\fBoddcomp\fR\ 'u \fBoddcomp\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-fullwindow\ \fR\fB\fItoggle\fR\fR \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-ignorebz\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBoddcomp\fR\ 'u \fBoddcomp\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBoddcomp\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Composition" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-infile\fR \fIinfile\fR .RS 4 This is a file in the format of the output produced by \*(Aqcompseq\*(Aq that is used to set the minimum frequencies of words in this analysis\&. .RE .SS "Required section" .PP \fB\-fullwindow\fR \fItoggle\fR .RS 4 Set this option on (Y) if you want the window size to be set to the length of the current protein\&. Otherwise, leave this option unset, in which case you\*(Aqll be prompted for a window size to use\&. Default value: N .RE .PP \fB\-window\fR \fIinteger\fR .RS 4 This is the size of window in which to count\&. Thus if you want to count frequencies in a 40 aa stretch you should enter 40 here\&. Default value: 30 .RE .SS "Advanced section" .PP \fB\-ignorebz\fR \fIboolean\fR .RS 4 The amino acid code B represents Asparagine or Aspartic acid and the code Z represents Glutamine or Glutamic acid\&. These are not commonly used codes and you may wish not to count words containing them, just noting them in the count of \*(AqOther\*(Aq words\&. Default value: Y .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 This is the results file\&. .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP oddcomp is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/embossversion.1e0000644000000000000000000000502012214054043014076 0ustar '\" t .\" Title: EMBOSSVERSION .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "EMBOSSVERSION" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" embossversion \- Reports the current EMBOSS version number .SH "SYNOPSIS" .HP \w'\fBembossversion\fR\ 'u \fBembossversion\fR [\fB\-full\ \fR\fB\fIboolean\fR\fR] [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] .HP \w'\fBembossversion\fR\ 'u \fBembossversion\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBembossversion\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils" command group(s)\&. .SH "OPTIONS" .SS "Additional section" .PP \fB\-full\fR \fIboolean\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP embossversion is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/trimest.1e0000644000000000000000000001141712214054043012676 0ustar '\" t .\" Title: TRIMEST .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "TRIMEST" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" trimest \- Remove poly\-A tails from nucleotide sequences .SH "SYNOPSIS" .HP \w'\fBtrimest\fR\ 'u \fBtrimest\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-minlength\ \fR\fB\fIinteger\fR\fR] [\fB\-mismatches\ \fR\fB\fIinteger\fR\fR] [\fB\-reverse\ \fR\fB\fIboolean\fR\fR] [\fB\-tolower\ \fR\fB\fItoggle\fR\fR] \fB\-fiveprime\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBtrimest\fR\ 'u \fBtrimest\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBtrimest\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Functional sites,Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Additional section" .PP \fB\-minlength\fR \fIinteger\fR .RS 4 This is the minimum length that a poly\-A (or poly\-T) tail must have before it is removed\&. If there are mismatches in the tail than there must be at least this length of poly\-A tail before the mismatch for the mismatch to be considered part of the tail\&. Default value: 4 .RE .PP \fB\-mismatches\fR \fIinteger\fR .RS 4 If there are this number or fewer contiguous non\-A bases in a poly\-A tail then, if there are \*(Aq\-minlength\*(Aq \*(AqA\*(Aq bases before them, they will be considered part of the tail and removed \&. For example the terminal 4 A\*(Aqs of GCAGAAAA would be removed with the default values of \-minlength=4 and \-mismatches=1 (There are not at least 4 A\*(Aqs before the last \*(AqG\*(Aq and so only the A\*(Aqs after it are considered to be part of the tail)\&. The terminal 9 bases of GCAAAAGAAAA would be removed; There are at least \-minlength A\*(Aqs preceeding the last \*(AqG\*(Aq, so it is part of the tail\&. Default value: 1 .RE .PP \fB\-reverse\fR \fIboolean\fR .RS 4 When a poly\-T region at the 5\*(Aq end of the sequence is found and removed, it is likely that the sequence is in the reverse sense\&. This option will change the sequence to the forward sense when it is written out\&. If this option is not set, then the sense will not be changed\&. Default value: Y .RE .PP \fB\-tolower\fR \fItoggle\fR .RS 4 The poly\-A region can be \*(Aqmasked\*(Aq by converting the sequence characters to lower\-case\&. Some non\-EMBOSS programs e\&.g\&. fasta can interpret this as a masked region\&. The sequence is unchanged apart from the case change\&. You might like to ensure that the whole sequence is in upper\-case before masking the specified regions to lower\-case by using the \*(Aq\-supper\*(Aq sequence qualifier\&. Default value: N .RE .SS "Advanced section" .PP \fB\-fiveprime\fR \fIboolean\fR .RS 4 If this is set true, then the 5\*(Aq end of the sequence is inspected for poly\-T tails\&. These will be removed if they are longer than any 3\*(Aq poly\-A tails\&. If this is false, then the 5\*(Aq end is ignored\&. Default value: Y .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP trimest is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/restover.1e0000644000000000000000000001033112214054043013052 0ustar '\" t .\" Title: RESTOVER .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "RESTOVER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" restover \- Find restriction enzymes producing a specific overhang .SH "SYNOPSIS" .HP \w'\fBrestover\fR\ 'u \fBrestover\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-datafile\ \fR\fB\fIdatafile\fR\fR \fB\-mfile\ \fR\fB\fIdatafile\fR\fR \fB\-seqcomp\ \fR\fB\fIstring\fR\fR \fB\-min\ \fR\fB\fIinteger\fR\fR \fB\-max\ \fR\fB\fIinteger\fR\fR \fB\-single\ \fR\fB\fIboolean\fR\fR \fB\-threeprime\ \fR\fB\fIboolean\fR\fR \fB\-blunt\ \fR\fB\fIboolean\fR\fR \fB\-sticky\ \fR\fB\fIboolean\fR\fR \fB\-ambiguity\ \fR\fB\fIboolean\fR\fR \fB\-plasmid\ \fR\fB\fIboolean\fR\fR \fB\-methylation\ \fR\fB\fIboolean\fR\fR \fB\-commercial\ \fR\fB\fIboolean\fR\fR \fB\-html\ \fR\fB\fIboolean\fR\fR \fB\-limit\ \fR\fB\fIboolean\fR\fR \fB\-alphabetic\ \fR\fB\fIboolean\fR\fR \fB\-fragments\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBrestover\fR\ 'u \fBrestover\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBrestover\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Restriction" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-datafile\fR \fIdatafile\fR .RS 4 .RE .PP \fB\-mfile\fR \fIdatafile\fR .RS 4 Default value: Emethylsites\&.dat .RE .SS "Required section" .PP \fB\-seqcomp\fR \fIstring\fR .RS 4 .RE .SS "Advanced section" .PP \fB\-min\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-max\fR \fIinteger\fR .RS 4 Default value: 2000000000 .RE .PP \fB\-single\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-threeprime\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-blunt\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-sticky\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-ambiguity\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-plasmid\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-methylation\fR \fIboolean\fR .RS 4 If this is set then RE recognition sites will not match methylated bases\&. Default value: N .RE .PP \fB\-commercial\fR \fIboolean\fR .RS 4 Default value: Y .RE .SS "Output section" .PP \fB\-html\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-limit\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-alphabetic\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-fragments\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP restover is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/profit.1e0000644000000000000000000000506112214054043012510 0ustar '\" t .\" Title: PROFIT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PROFIT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" profit \- Scan one or more sequences with a simple frequency matrix .SH "SYNOPSIS" .HP \w'\fBprofit\fR\ 'u \fBprofit\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBprofit\fR\ 'u \fBprofit\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBprofit\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Profiles,Protein:Profiles" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP profit is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/sixpack.1e0000644000000000000000000001320312214054043012644 0ustar '\" t .\" Title: SIXPACK .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SIXPACK" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" sixpack \- Display a DNA sequence with 6\-frame translation and ORFs .SH "SYNOPSIS" .HP \w'\fBsixpack\fR\ 'u \fBsixpack\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-table\ \fR\fB\fIlist\fR\fR] [\fB\-firstorf\ \fR\fB\fIboolean\fR\fR] [\fB\-lastorf\ \fR\fB\fIboolean\fR\fR] [\fB\-mstart\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR \fB\-reverse\ \fR\fB\fIboolean\fR\fR \fB\-orfminsize\ \fR\fB\fIinteger\fR\fR \fB\-uppercase\ \fR\fB\fIrange\fR\fR \fB\-highlight\ \fR\fB\fIrange\fR\fR \fB\-number\ \fR\fB\fIboolean\fR\fR \fB\-width\ \fR\fB\fIinteger\fR\fR \fB\-length\ \fR\fB\fIinteger\fR\fR \fB\-margin\ \fR\fB\fIinteger\fR\fR \fB\-name\ \fR\fB\fIboolean\fR\fR \fB\-description\ \fR\fB\fIboolean\fR\fR \fB\-offset\ \fR\fB\fIinteger\fR\fR \fB\-html\ \fR\fB\fIboolean\fR\fR .HP \w'\fBsixpack\fR\ 'u \fBsixpack\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBsixpack\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Gene finding,Nucleic:Translation,Display" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .SS "Additional section" .PP \fB\-table\fR \fIlist\fR .RS 4 Genetics code used for the translation .RE .PP \fB\-firstorf\fR \fIboolean\fR .RS 4 Count the beginning of a sequence as a possible ORF, even if it\*(Aqs inferior to the minimal ORF size\&. Default value: Y .RE .PP \fB\-lastorf\fR \fIboolean\fR .RS 4 Count the end of a sequence as a possible ORF, even if it\*(Aqs not finishing with a STOP, or inferior to the minimal ORF size\&. Default value: Y .RE .PP \fB\-mstart\fR \fIboolean\fR .RS 4 Displays only ORFs starting with an M\&. Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 ORF sequence output .RE .PP \fB\-reverse\fR \fIboolean\fR .RS 4 Display also the translation of the DNA sequence in the 3 reverse frames Default value: Y .RE .PP \fB\-orfminsize\fR \fIinteger\fR .RS 4 Minimum size of Open Reading Frames (ORFs) to display in the translations\&. Default value: 1 .RE .PP \fB\-uppercase\fR \fIrange\fR .RS 4 Regions to put in uppercase\&. If this is left blank, then the sequence case is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 24\-45, 56\-78 1:45, 67=99;765\&.\&.888 1,5,8,10,23,45,57,99 .RE .PP \fB\-highlight\fR \fIrange\fR .RS 4 Regions to colour if formatting for HTML\&. If this is left blank, then the sequence is left alone\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are followed by any valid HTML font colour\&. Examples of region specifications are: 24\-45 blue 56\-78 orange 1\-100 green 120\-156 red A file of ranges to colour (one range per line) can be specified as \*(Aq@filename\*(Aq\&. .RE .PP \fB\-number\fR \fIboolean\fR .RS 4 Number the sequence at the beginning and the end of each line\&. Default value: Y .RE .PP \fB\-width\fR \fIinteger\fR .RS 4 Number of nucleotides displayed on each line Default value: 60 .RE .PP \fB\-length\fR \fIinteger\fR .RS 4 .RE .PP \fB\-margin\fR \fIinteger\fR .RS 4 Default value: 10 .RE .PP \fB\-name\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to display the ID name of the sequence\&. Default value: Y .RE .PP \fB\-description\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to display the description of the sequence\&. Default value: Y .RE .PP \fB\-offset\fR \fIinteger\fR .RS 4 Number from which you want the DNA sequence to be numbered\&. Default value: 1 .RE .PP \fB\-html\fR \fIboolean\fR .RS 4 Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP sixpack is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/seealso.1e0000644000000000000000000001335712214054043012647 0ustar '\" t .\" Title: SEEALSO .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SEEALSO" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" seealso \- Finds programs with similar function to a specified program .SH "SYNOPSIS" .HP \w'\fBseealso\fR\ 'u \fBseealso\fR \fB\-search\ \fR\fB\fIstring\fR\fR [\fB\-explode\ \fR\fB\fIboolean\fR\fR] \fB\-emboss\ \fR\fB\fIboolean\fR\fR \fB\-embassy\ \fR\fB\fIboolean\fR\fR \fB\-showembassy\ \fR\fB\fIstring\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fItoggle\fR\fR] [\fB\-groups\ \fR\fB\fIboolean\fR\fR] \fB\-colon\ \fR\fB\fIboolean\fR\fR .HP \w'\fBseealso\fR\ 'u \fBseealso\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBseealso\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Documentation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-search\fR \fIstring\fR .RS 4 Enter the name of an EMBOSS program .RE .SS "Additional section" .PP \fB\-explode\fR \fIboolean\fR .RS 4 The groups that EMBOSS applications belong to have two forms, exploded and not exploded\&. The exploded group names are more numerous and often vaguely phrased than the non\-exploded ones\&. The exploded names are formed from definitions of the group names that start like NAME1:NAME2 and which are then expanded into many combinations of the names as: \*(AqNAME1\*(Aq, \*(AqNAME2\*(Aq, \*(AqNAME1 NAME2\*(Aq, NAME2 NAME1\*(Aq\&. The non\-expanded names are simply like: \*(AqNAME1 NAME2\*(Aq\&. Using expanded group names will find many more programs which share at least some of the expanded names than using the non\-exploded names and so you will get more programs reported as sharing a similar function than you will if you specify that you wish to use non\-exploded names Default value: N .RE .SS "Advanced section" .PP \fB\-emboss\fR \fIboolean\fR .RS 4 If you use this option then EMBOSS program documentation will be searched\&. If this option is set to be false, then only the EMBASSY programs will be searched (if the \-embassy option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y .RE .PP \fB\-embassy\fR \fIboolean\fR .RS 4 If you use this option then EMBASSY program documentation will be searched\&. If this option is set to be false, then only the EMBOSS programs will be searched (if the \-emboss option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y .RE .PP \fB\-showembassy\fR \fIstring\fR .RS 4 If you use this option then this EMBASSY package program documentation will be searched\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .SS "Html section" .PP \fB\-html\fR \fItoggle\fR .RS 4 If you are sending the output to a file, this will format it for displaying as a table in a WWW document\&. Default value: N .RE .PP \fB\-groups\fR \fIboolean\fR .RS 4 If you use this option, then only the group names will output to the file Default value: N .RE .PP \fB\-colon\fR \fIboolean\fR .RS 4 The groups that EMBOSS applications belong to have up to two levels, for example the primary group \*(AqALIGNMENT\*(Aq has several sub\-groups, or second\-level groups, e\&.g\&.: CONSENSUS, DIFFERENCES, DOT PLOTS, GLOBAL, LOCAL, MULTIPLE\&. To aid programs that parse the output of seealso that require the names of these subgroups, a colon \*(Aq:\*(Aq will be placed between the first and second level of the group name if this option is true\&. Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP seealso is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/domtestd.1e0000644000000000000000000000454412214054043013035 0ustar '\" t .\" Title: DOMTESTD .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DOMTESTD" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" domtestd \- Create some XML and search for an element .SH "SYNOPSIS" .HP \w'\fBdomtestd\fR\ 'u \fBdomtestd\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBdomtestd\fR\ 'u \fBdomtestd\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdomtestd\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP domtestd is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/docxmlwell.1e0000644000000000000000000000503712214054043013362 0ustar '\" t .\" Title: DOCXMLWELL .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DOCXMLWELL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" docxmlwell \- Check an XML document is well formed .SH "SYNOPSIS" .HP \w'\fBdocxmlwell\fR\ 'u \fBdocxmlwell\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBdocxmlwell\fR\ 'u \fBdocxmlwell\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdocxmlwell\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Misc" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .SS "Required section" .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-logfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP docxmlwell is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/dotpath.1e0000644000000000000000000000572712214054043012661 0ustar '\" t .\" Title: DOTPATH .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DOTPATH" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" dotpath \- Draw a non\-overlapping wordmatch dotplot of two sequences .SH "SYNOPSIS" .HP \w'\fBdotpath\fR\ 'u \fBdotpath\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR \fB\-wordsize\ \fR\fB\fIinteger\fR\fR [\fB\-overlaps\ \fR\fB\fIboolean\fR\fR] [\fB\-boxit\ \fR\fB\fIboolean\fR\fR] \fB\-graph\ \fR\fB\fIgraph\fR\fR .HP \w'\fBdotpath\fR\ 'u \fBdotpath\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdotpath\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Dot plots" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-asequence\fR \fIsequence\fR .RS 4 .RE .PP \fB\-bsequence\fR \fIsequence\fR .RS 4 .RE .SS "Required section" .PP \fB\-wordsize\fR \fIinteger\fR .RS 4 Default value: 4 .RE .SS "Output section" .PP \fB\-overlaps\fR \fIboolean\fR .RS 4 Displays the overlapping matches (in red) as well as the minimal set of non\-overlapping matches Default value: N .RE .PP \fB\-boxit\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-graph\fR \fIgraph\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP dotpath is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/origsplitter.1e0000644000000000000000000000551012214054043013733 0ustar '\" t .\" Title: ORIGSPLITTER .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ORIGSPLITTER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" origsplitter \- Split a sequence into (overlapping) smaller sequences .SH "SYNOPSIS" .HP \w'\fBorigsplitter\fR\ 'u \fBorigsplitter\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-size\ \fR\fB\fIinteger\fR\fR] [\fB\-overlap\ \fR\fB\fIinteger\fR\fR] \fB\-addoverlap\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBorigsplitter\fR\ 'u \fBorigsplitter\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBorigsplitter\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Additional section" .PP \fB\-size\fR \fIinteger\fR .RS 4 Default value: 10000 .RE .PP \fB\-overlap\fR \fIinteger\fR .RS 4 .RE .SS "Advanced section" .PP \fB\-addoverlap\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP origsplitter is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/martseqs.1e0000644000000000000000000000526412214054043013051 0ustar '\" t .\" Title: MARTSEQS .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "MARTSEQS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" martseqs \- Show Biomart datasets that can return sequences .SH "SYNOPSIS" .HP \w'\fBmartseqs\fR\ 'u \fBmartseqs\fR \fB\-host\ \fR\fB\fIstring\fR\fR \fB\-path\ \fR\fB\fIstring\fR\fR \fB\-port\ \fR\fB\fIinteger\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBmartseqs\fR\ 'u \fBmartseqs\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBmartseqs\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-host\fR \fIstring\fR .RS 4 Default value: www\&.biomart\&.org .RE .PP \fB\-path\fR \fIstring\fR .RS 4 Default value: /biomart/martservice .RE .PP \fB\-port\fR \fIinteger\fR .RS 4 Default value: 80 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP martseqs is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/polydot.1e0000644000000000000000000000622612214054043012703 0ustar '\" t .\" Title: POLYDOT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "POLYDOT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" polydot \- Draw dotplots for all\-against\-all comparison of a sequence set .SH "SYNOPSIS" .HP \w'\fBpolydot\fR\ 'u \fBpolydot\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR \fB\-wordsize\ \fR\fB\fIinteger\fR\fR \fB\-gap\ \fR\fB\fIinteger\fR\fR [\fB\-boxit\ \fR\fB\fIboolean\fR\fR] [\fB\-dumpfeat\ \fR\fB\fItoggle\fR\fR] \fB\-outfeat\ \fR\fB\fIfeatout\fR\fR \fB\-graph\ \fR\fB\fIgraph\fR\fR .HP \w'\fBpolydot\fR\ 'u \fBpolydot\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBpolydot\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Dot plots" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequences\fR \fIseqset\fR .RS 4 File containing a sequence alignment .RE .SS "Required section" .PP \fB\-wordsize\fR \fIinteger\fR .RS 4 Default value: 6 .RE .SS "Output section" .PP \fB\-gap\fR \fIinteger\fR .RS 4 This specifies the size of the gap that is used to separate the individual dotplots in the display\&. The size is measured in residues, as displayed in the output\&. Default value: 10 .RE .PP \fB\-boxit\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-dumpfeat\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-outfeat\fR \fIfeatout\fR .RS 4 .RE .PP \fB\-graph\fR \fIgraph\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP polydot is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/codcmp.1e0000644000000000000000000000507212214054043012454 0ustar '\" t .\" Title: CODCMP .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "CODCMP" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" codcmp \- Codon usage table comparison .SH "SYNOPSIS" .HP \w'\fBcodcmp\fR\ 'u \fBcodcmp\fR \fB\-first\ \fR\fB\fIcodon\fR\fR \fB\-second\ \fR\fB\fIcodon\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBcodcmp\fR\ 'u \fBcodcmp\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBcodcmp\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Codon usage" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-first\fR \fIcodon\fR .RS 4 First codon usage file .RE .PP \fB\-second\fR \fIcodon\fR .RS 4 Second codon usage file for comparison .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP codcmp is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/compseq.1e0000644000000000000000000001277012214054043012661 0ustar '\" t .\" Title: COMPSEQ .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "COMPSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" compseq \- Calculate the composition of unique words in sequences .SH "SYNOPSIS" .HP \w'\fBcompseq\fR\ 'u \fBcompseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-infile\ \fR\fB\fIinfile\fR\fR] \fB\-word\ \fR\fB\fIinteger\fR\fR [\fB\-frame\ \fR\fB\fIinteger\fR\fR] \fB\-ignorebz\ \fR\fB\fIboolean\fR\fR \fB\-reverse\ \fR\fB\fIboolean\fR\fR [\fB\-calcfreq\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-zerocount\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBcompseq\fR\ 'u \fBcompseq\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBcompseq\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Composition,Protein:Composition" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-infile\fR \fIinfile\fR .RS 4 This is a file previously produced by \*(Aqcompseq\*(Aq that can be used to set the expected frequencies of words in this analysis\&. The word size in the current run must be the same as the one in this results file\&. Obviously, you should use a file produced from protein sequences if you are counting protein sequence word frequencies, and you must use one made from nucleotide frequencies if you are analysing a nucleotide sequence\&. .RE .SS "Required section" .PP \fB\-word\fR \fIinteger\fR .RS 4 This is the size of word (n\-mer) to count\&. Thus if you want to count codon frequencies for a nucleotide sequence, you should enter 3 here\&. Default value: 2 .RE .SS "Additional section" .PP \fB\-frame\fR \fIinteger\fR .RS 4 The normal behaviour of \*(Aqcompseq\*(Aq is to count the frequencies of all words that occur by moving a window of length \*(Aqword\*(Aq up by one each time\&. This option allows you to move the window up by the length of the word each time, skipping over the intervening words\&. You can count only those words that occur in a single frame of the word by setting this value to a number other than zero\&. If you set it to 1 it will only count the words in frame 1, 2 will only count the words in frame 2 and so on\&. .RE .PP \fB\-ignorebz\fR \fIboolean\fR .RS 4 The amino acid code B represents Asparagine or Aspartic acid and the code Z represents Glutamine or Glutamic acid\&. These are not commonly used codes and you may wish not to count words containing them, just noting them in the count of \*(AqOther\*(Aq words\&. Default value: Y .RE .PP \fB\-reverse\fR \fIboolean\fR .RS 4 Set this to be true if you also wish to also count words in the reverse complement of a nucleic sequence\&. Default value: N .RE .PP \fB\-calcfreq\fR \fIboolean\fR .RS 4 If this is set true then the expected frequencies of words are calculated from the observed frequency of single bases or residues in the sequences\&. If you are reporting a word size of 1 (single bases or residues) then there is no point in using this option because the calculated expected frequency will be equal to the observed frequency\&. Calculating the expected frequencies like this will give an approximation of the expected frequencies that you might get by using an input file of frequencies produced by a previous run of this program\&. If an input file of expected word frequencies has been specified then the values from that file will be used instead of this calculation of expected frequency from the sequence, even if \*(Aqcalcfreq\*(Aq is set to be true\&. Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 This is the results file\&. .RE .PP \fB\-zerocount\fR \fIboolean\fR .RS 4 You can make the output results file much smaller if you do not display the words with a zero count\&. Default value: Y .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP compseq is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/dbtell.1e0000644000000000000000000000543412214054043012457 0ustar '\" t .\" Title: DBTELL .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DBTELL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" dbtell \- Display information about a public database .SH "SYNOPSIS" .HP \w'\fBdbtell\fR\ 'u \fBdbtell\fR \fB\-database\ \fR\fB\fIstring\fR\fR [\fB\-full\ \fR\fB\fIboolean\fR\fR] [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] .HP \w'\fBdbtell\fR\ 'u \fBdbtell\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdbtell\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data resources" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-database\fR \fIstring\fR .RS 4 The name of the database defined locally for use by EMBOSS\&. .RE .SS "Additional section" .PP \fB\-full\fR \fIboolean\fR .RS 4 The default behaviour is to report for relevant databases only basic information from the EMBOSS database definition Default value: N .RE .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP dbtell is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/edamclean.1e0000644000000000000000000000612212214054043013115 0ustar '\" t .\" Title: EDAMCLEAN .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "EDAMCLEAN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" edamclean \- Validate and fix EDAM OBO ontology .SH "SYNOPSIS" .HP \w'\fBedamclean\fR\ 'u \fBedamclean\fR \fB\-edaminfile\ \fR\fB\fIinfile\fR\fR \fB\-taxdirectory\ \fR\fB\fIdirectory\fR\fR \fB\-mode\ \fR\fB\fIselection\fR\fR \fB\-edamoutfile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR \fB\-xmlfile\ \fR\fB\fIoutfile\fR\fR \fB\-xmloutdir\ \fR\fB\fIoutdir\fR\fR .HP \w'\fBedamclean\fR\ 'u \fBedamclean\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBedamclean\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-edaminfile\fR \fIinfile\fR .RS 4 Default value: /homes/jison/edam/EDAM\&.obo .RE .PP \fB\-taxdirectory\fR \fIdirectory\fR .RS 4 .RE .SS "Required section" .PP \fB\-mode\fR \fIselection\fR .RS 4 Default value: Report only .RE .SS "Advanced section" .SS "Output section" .PP \fB\-edamoutfile\fR \fIoutfile\fR .RS 4 Default value: EDAM_out\&.obo .RE .PP \fB\-logfile\fR \fIoutfile\fR .RS 4 Default value: EDAM_out\&.log .RE .PP \fB\-xmlfile\fR \fIoutfile\fR .RS 4 Default value: EDAM_out\&.xml .RE .PP \fB\-xmloutdir\fR \fIoutdir\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP edamclean is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/xmltoxml.1e0000644000000000000000000000621612214054043013074 0ustar '\" t .\" Title: XMLTOXML .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "XMLTOXML" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" xmltoxml \- Convert an XML document to a different format .SH "SYNOPSIS" .HP \w'\fBxmltoxml\fR\ 'u \fBxmltoxml\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-type\ \fR\fB\fIlist\fR\fR \fB\-seq\ \fR\fB\fIlist\fR\fR \fB\-feat\ \fR\fB\fIlist\fR\fR \fB\-align\ \fR\fB\fIlist\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBxmltoxml\fR\ 'u \fBxmltoxml\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBxmltoxml\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Misc" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .SS "Required section" .PP \fB\-type\fR \fIlist\fR .RS 4 You must specify the type of file content so that appropriate output format options may be generated\&. .RE .PP \fB\-seq\fR \fIlist\fR .RS 4 This option sets the XML format of a sequence output file\&. Default value: X .RE .PP \fB\-feat\fR \fIlist\fR .RS 4 This option sets the XML format of a sequence feature output file\&. Default value: X .RE .PP \fB\-align\fR \fIlist\fR .RS 4 This option sets the XML format of a sequence alignment output file\&. Default value: X .RE .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP xmltoxml is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/tfm.1e0000644000000000000000000000575012214054043012000 0ustar '\" t .\" Title: TFM .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "TFM" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" tfm \- Displays full documentation for an application .SH "SYNOPSIS" .HP \w'\fBtfm\fR\ 'u \fBtfm\fR \fB\-program\ \fR\fB\fIstring\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fIboolean\fR\fR] [\fB\-more\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBtfm\fR\ 'u \fBtfm\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBtfm\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Documentation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-program\fR \fIstring\fR .RS 4 Enter the name of an EMBOSS program .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .PP \fB\-html\fR \fIboolean\fR .RS 4 This will format the output for displaying as a WWW document\&. Default value: N .RE .PP \fB\-more\fR \fIboolean\fR .RS 4 This uses the standard UNIX utility \*(Aqmore\*(Aq to display the text page\-by\-page, waiting for you to read one screen\-full before going on to the next page\&. When you have finished reading a page, press the SPACE bar to proceed to the next page\&. Default value: @(!$(html)) .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP tfm is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/wossparam.1e0000644000000000000000000001603512214054043013224 0ustar '\" t .\" Title: WOSSPARAM .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "WOSSPARAM" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" wossparam \- Finds programs by EDAM parameter .SH "SYNOPSIS" .HP \w'\fBwossparam\fR\ 'u \fBwossparam\fR \fB\-identifier\ \fR\fB\fIstring\fR\fR [\fB\-explode\ \fR\fB\fIboolean\fR\fR] [\fB\-showkeywords\ \fR\fB\fIboolean\fR\fR] \fB\-sensitive\ \fR\fB\fIboolean\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-emboss\ \fR\fB\fIboolean\fR\fR \fB\-embassy\ \fR\fB\fIboolean\fR\fR \fB\-showembassy\ \fR\fB\fIstring\fR\fR \fB\-colon\ \fR\fB\fIboolean\fR\fR \fB\-gui\ \fR\fB\fIboolean\fR\fR [\fB\-outfile\ \fR\fB\fIoutfile\fR\fR] [\fB\-html\ \fR\fB\fItoggle\fR\fR] [\fB\-groups\ \fR\fB\fIboolean\fR\fR] [\fB\-alphabetic\ \fR\fB\fIboolean\fR\fR] .HP \w'\fBwossparam\fR\ 'u \fBwossparam\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBwossparam\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Documentation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-identifier\fR \fIstring\fR .RS 4 .RE .SS "Additional section" .PP \fB\-explode\fR \fIboolean\fR .RS 4 The groups that EMBOSS applications belong to have two forms, exploded and not exploded\&. The exploded group names are more numerous and often vaguely phrased than the non\-exploded ones\&. The exploded names are formed from definitions of the group names that start like NAME1:NAME2 and which are then expanded into many combinations of the names as: \*(AqNAME1\*(Aq, \*(AqNAME2\*(Aq, \*(AqNAME1 NAME2\*(Aq, NAME2 NAME1\*(Aq\&. The non\-expanded names are simply like: \*(AqNAME1 NAME2\*(Aq\&. Default value: N .RE .PP \fB\-showkeywords\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Advanced section" .PP \fB\-sensitive\fR \fIboolean\fR .RS 4 By default, the query keywords are matched against the EDAM term names (and synonyms) only\&. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches\&. Default value: N .RE .PP \fB\-subclasses\fR \fIboolean\fR .RS 4 Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: Y .RE .PP \fB\-obsolete\fR \fIboolean\fR .RS 4 The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N .RE .PP \fB\-emboss\fR \fIboolean\fR .RS 4 If you use this option then EMBOSS program documentation will be searched\&. If this option is set to be false, then only the EMBASSY programs will be searched (if the \-embassy option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y .RE .PP \fB\-embassy\fR \fIboolean\fR .RS 4 If you use this option then EMBASSY program documentation will be searched\&. If this option is set to be false, then only the EMBOSS programs will be searched (if the \-emboss option is true)\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme Default value: Y .RE .PP \fB\-showembassy\fR \fIstring\fR .RS 4 If you use this option then this EMBASSY package program documentation will be searched\&. EMBASSY programs are not strictly part of EMBOSS, but use the same code libraries and share the same look and feel, but are generally developed by people who wish the programs to be outside of the GNU Public Licence scheme .RE .PP \fB\-colon\fR \fIboolean\fR .RS 4 The groups that EMBOSS applications belong to up to two levels, for example the primary group \*(AqALIGNMENT\*(Aq has several sub\-groups, or second\-level groups, e\&.g\&.: CONSENSUS, DIFFERENCES, DOT PLOTS, GLOBAL, LOCAL, MULTIPLE\&. To aid programs that parse the output of wossname that require the names of these subgroups, a colon \*(Aq:\*(Aq will be placed between the first and second level of the group name if this option is true\&. Note: This does not apply if the group names have been exploded with the \*(Aqexplode\*(Aq option\&. Default value: N .RE .PP \fB\-gui\fR \fIboolean\fR .RS 4 This option is intended to help those who are designing Graphical User Interfaces to the EMBOSS applications\&. Some EMBOSS programs are inappropriate for running in a GUI, these include other menu programs and interactive editors\&. This option allows you to only report those programs that can be run from a GUI Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .SS "Html section" .PP \fB\-html\fR \fItoggle\fR .RS 4 If you are sending the output to a file, this will format it for displaying as a table in a WWW document\&. Default value: N .RE .PP \fB\-groups\fR \fIboolean\fR .RS 4 If you use this option, then only the group names will be output to the file Default value: N .RE .PP \fB\-alphabetic\fR \fIboolean\fR .RS 4 If you use this option, then you will get a single list of the program names and descriptions instead of the programs being listed in their functional groups\&. Default value: N .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP wossparam is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/patmatmotifs.1e0000644000000000000000000000570512214054043013722 0ustar '\" t .\" Title: PATMATMOTIFS .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PATMATMOTIFS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" patmatmotifs \- Scan a protein sequence with motifs from the PROSITE database .SH "SYNOPSIS" .HP \w'\fBpatmatmotifs\fR\ 'u \fBpatmatmotifs\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-full\ \fR\fB\fIboolean\fR\fR] [\fB\-prune\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIreport\fR\fR .HP \w'\fBpatmatmotifs\fR\ 'u \fBpatmatmotifs\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBpatmatmotifs\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Motifs" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .SS "Additional section" .PP \fB\-full\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-prune\fR \fIboolean\fR .RS 4 Ignore simple patterns\&. If this is true then these simple post\-translational modification sites are not reported: myristyl, asn_glycosylation, camp_phospho_site, pkc_phospho_site, ck2_phospho_site, and tyr_phospho_site\&. Default value: Y .RE .SS "Output section" .PP \fB\-outfile\fR \fIreport\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP patmatmotifs is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/xmltransform.1e0000644000000000000000000000535712214054043013751 0ustar '\" t .\" Title: XMLTRANSFORM .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "XMLTRANSFORM" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" xmltransform \- Convert an XML document to a different format using a supplied XSLT file .SH "SYNOPSIS" .HP \w'\fBxmltransform\fR\ 'u \fBxmltransform\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-xslt\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBxmltransform\fR\ 'u \fBxmltransform\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBxmltransform\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Misc" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .PP \fB\-xslt\fR \fIinfile\fR .RS 4 .RE .SS "Required section" .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-logfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP xmltransform is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/chaos.1e0000644000000000000000000000471712214054043012311 0ustar '\" t .\" Title: CHAOS .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "CHAOS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" chaos \- Draw a chaos game representation plot for a nucleotide sequence .SH "SYNOPSIS" .HP \w'\fBchaos\fR\ 'u \fBchaos\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-graph\ \fR\fB\fIgraph\fR\fR .HP \w'\fBchaos\fR\ 'u \fBchaos\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBchaos\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Composition" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .SS "Output section" .PP \fB\-graph\fR \fIgraph\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP chaos is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/seqcount.1e0000644000000000000000000000467212214054043013055 0ustar '\" t .\" Title: SEQCOUNT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SEQCOUNT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" seqcount \- Reads and counts sequences .SH "SYNOPSIS" .HP \w'\fBseqcount\fR\ 'u \fBseqcount\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBseqcount\fR\ 'u \fBseqcount\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBseqcount\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP seqcount is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/testplot.1e0000644000000000000000000000503212214054043013061 0ustar '\" t .\" Title: TESTPLOT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "TESTPLOT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" testplot \- Test plot .SH "SYNOPSIS" .HP \w'\fBtestplot\fR\ 'u \fBtestplot\fR \fB\-points\ \fR\fB\fIinteger\fR\fR \fB\-overlap\ \fR\fB\fIboolean\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR .HP \w'\fBtestplot\fR\ 'u \fBtestplot\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBtestplot\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Test" command group(s)\&. .SH "OPTIONS" .SS "Required section" .PP \fB\-points\fR \fIinteger\fR .RS 4 Default value: 90 .RE .SS "Output section" .PP \fB\-overlap\fR \fIboolean\fR .RS 4 Default value: y .RE .PP \fB\-graph\fR \fIxygraph\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP testplot is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/dbigcg.1e0000644000000000000000000000743612214054043012434 0ustar '\" t .\" Title: DBIGCG .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DBIGCG" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" dbigcg \- Index a GCG formatted database .SH "SYNOPSIS" .HP \w'\fBdbigcg\fR\ 'u \fBdbigcg\fR \fB\-dbname\ \fR\fB\fIstring\fR\fR \fB\-idformat\ \fR\fB\fIlist\fR\fR \fB\-directory\ \fR\fB\fIdirectory\fR\fR \fB\-filenames\ \fR\fB\fIstring\fR\fR \fB\-release\ \fR\fB\fIstring\fR\fR \fB\-date\ \fR\fB\fIstring\fR\fR \fB\-fields\ \fR\fB\fIlist\fR\fR \fB\-exclude\ \fR\fB\fIstring\fR\fR \fB\-maxindex\ \fR\fB\fIinteger\fR\fR \fB\-sortoptions\ \fR\fB\fIstring\fR\fR \fB\-systemsort\ \fR\fB\fIboolean\fR\fR \fB\-cleanup\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-indexoutdir\ \fR\fB\fIoutdir\fR\fR .HP \w'\fBdbigcg\fR\ 'u \fBdbigcg\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdbigcg\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database indexing" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-dbname\fR \fIstring\fR .RS 4 .RE .PP \fB\-idformat\fR \fIlist\fR .RS 4 Default value: EMBL .RE .PP \fB\-directory\fR \fIdirectory\fR .RS 4 Default value: \&. .RE .PP \fB\-filenames\fR \fIstring\fR .RS 4 Default value: *\&.seq .RE .SS "Required section" .PP \fB\-release\fR \fIstring\fR .RS 4 Default value: 0\&.0 .RE .PP \fB\-date\fR \fIstring\fR .RS 4 Default value: 00/00/00 .RE .SS "Advanced section" .PP \fB\-fields\fR \fIlist\fR .RS 4 Default value: acc .RE .PP \fB\-exclude\fR \fIstring\fR .RS 4 .RE .PP \fB\-maxindex\fR \fIinteger\fR .RS 4 .RE .PP \fB\-sortoptions\fR \fIstring\fR .RS 4 Sort options, typically \*(Aq\-T \&.\*(Aq to use current directory for work files and \*(Aq\-k 1,1\*(Aq to force GNU sort to use the first field Default value: \-T \&. \-k 1,1 .RE .PP \fB\-systemsort\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-cleanup\fR \fIboolean\fR .RS 4 Default value: Y .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-indexoutdir\fR \fIoutdir\fR .RS 4 Default value: \&. .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP dbigcg is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/supermatcher.1e0000644000000000000000000000735112214054043013713 0ustar '\" t .\" Title: SUPERMATCHER .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SUPERMATCHER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" supermatcher \- Calculate approximate local pair\-wise alignments of larger sequences .SH "SYNOPSIS" .HP \w'\fBsupermatcher\fR\ 'u \fBsupermatcher\fR \fB\-asequence\ \fR\fB\fIseqall\fR\fR \fB\-bsequence\ \fR\fB\fIseqset\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] [\fB\-minscore\ \fR\fB\fIfloat\fR\fR] \fB\-gapopen\ \fR\fB\fIfloat\fR\fR \fB\-gapextend\ \fR\fB\fIfloat\fR\fR [\fB\-width\ \fR\fB\fIinteger\fR\fR] [\fB\-wordlen\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIalign\fR\fR [\fB\-errorfile\ \fR\fB\fIoutfile\fR\fR] .HP \w'\fBsupermatcher\fR\ 'u \fBsupermatcher\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBsupermatcher\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Local" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-asequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-bsequence\fR \fIseqset\fR .RS 4 .RE .PP \fB\-datafile\fR \fImatrixf\fR .RS 4 This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&. .RE .PP \fB\-minscore\fR \fIfloat\fR .RS 4 Minimum alignment score to report an alignment\&. .RE .SS "Required section" .PP \fB\-gapopen\fR \fIfloat\fR .RS 4 Default value: @($(acdprotein)? 10\&.0 : 10\&.0) .RE .PP \fB\-gapextend\fR \fIfloat\fR .RS 4 Default value: @($(acdprotein)? 0\&.5 : 0\&.5) .RE .SS "Additional section" .PP \fB\-width\fR \fIinteger\fR .RS 4 Default value: 16 .RE .PP \fB\-wordlen\fR \fIinteger\fR .RS 4 Default value: 6 .RE .SS "Output section" .PP \fB\-outfile\fR \fIalign\fR .RS 4 .RE .PP \fB\-errorfile\fR \fIoutfile\fR .RS 4 Error file to be written to for failed alignments Default value: supermatcher\&.error .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP supermatcher is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/goname.1e0000644000000000000000000000613512214054043012456 0ustar '\" t .\" Title: GONAME .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "GONAME" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" goname \- Find GO ontology terms by name .SH "SYNOPSIS" .HP \w'\fBgoname\fR\ 'u \fBgoname\fR \fB\-query\ \fR\fB\fIstring\fR\fR [\fB\-namespace\ \fR\fB\fIlist\fR\fR] \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-goname\ \fR\fB\fIoutobo\fR\fR .HP \w'\fBgoname\fR\ 'u \fBgoname\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBgoname\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:GO,Data retrieval:Ontology data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-query\fR \fIstring\fR .RS 4 .RE .SS "Additional section" .PP \fB\-namespace\fR \fIlist\fR .RS 4 By default all terms are returned\&. Searches can be limited to one or a few namespaces\&. Default value: * .RE .SS "Advanced section" .PP \fB\-subclasses\fR \fIboolean\fR .RS 4 Extend the query matches to include all terms which are specialisations (GO sub\-classes) of the matched type\&. Default value: N .RE .PP \fB\-obsolete\fR \fIboolean\fR .RS 4 The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N .RE .SS "Output section" .PP \fB\-goname\fR \fIoutobo\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP goname is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/maskseq.1e0000644000000000000000000000733012214054043012652 0ustar '\" t .\" Title: MASKSEQ .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "MASKSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" maskseq \- Write a sequence with masked regions .SH "SYNOPSIS" .HP \w'\fBmaskseq\fR\ 'u \fBmaskseq\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-regions\ \fR\fB\fIrange\fR\fR [\fB\-tolower\ \fR\fB\fItoggle\fR\fR] \fB\-maskchar\ \fR\fB\fIstring\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR .HP \w'\fBmaskseq\fR\ 'u \fBmaskseq\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBmaskseq\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .SS "Required section" .PP \fB\-regions\fR \fIrange\fR .RS 4 Regions to mask\&. A set of regions is specified by a set of pairs of positions\&. The positions are integers\&. They are separated by any non\-digit, non\-alpha character\&. Examples of region specifications are: 24\-45, 56\-78 1:45, 67=99;765\&.\&.888 1,5,8,10,23,45,57,99 .RE .SS "Additional section" .PP \fB\-tolower\fR \fItoggle\fR .RS 4 The region can be \*(Aqmasked\*(Aq by converting the sequence characters to lower\-case, some non\-EMBOSS programs e\&.g\&. fasta can interpret this as a masked region\&. The sequence is unchanged apart from the case change\&. You might like to ensure that the whole sequence is in upper\-case before masking the specified regions to lower\-case by using the \*(Aq\-supper\*(Aq flag\&. Default value: N .RE .PP \fB\-maskchar\fR \fIstring\fR .RS 4 Character to use when masking\&. Default is \*(AqX\*(Aq for protein sequences, \*(AqN\*(Aq for nucleic sequences\&. If the mask character is set to be the SPACE character or a null character, then the sequence is \*(Aqmasked\*(Aq by changing it to lower\-case, just as with the \*(Aq\-lowercase\*(Aq flag\&. Default value: @($(acdprotein)?X:N) .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqout\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP maskseq is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/eprimer32.1e0000644000000000000000000006766312214054043013035 0ustar '\" t .\" Title: EPRIMER32 .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "EPRIMER32" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" eprimer32 \- Picks PCR primers and hybridization oligos .SH "SYNOPSIS" .HP \w'\fBeprimer32\fR\ 'u \fBeprimer32\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-primer\ \fR\fB\fItoggle\fR\fR] \fB\-task\ \fR\fB\fIlist\fR\fR [\fB\-hybridprobe\ \fR\fB\fItoggle\fR\fR] \fB\-mishyblibraryfile\ \fR\fB\fIinfile\fR\fR \fB\-mispriminglibraryfile\ \fR\fB\fIinfile\fR\fR [\fB\-numreturn\ \fR\fB\fIinteger\fR\fR] [\fB\-includedregion\ \fR\fB\fIrange\fR\fR] [\fB\-targetregion\ \fR\fB\fIrange\fR\fR] [\fB\-excludedregion\ \fR\fB\fIrange\fR\fR] [\fB\-forwardinput\ \fR\fB\fIstring\fR\fR] [\fB\-reverseinput\ \fR\fB\fIstring\fR\fR] \fB\-gcclamp\ \fR\fB\fIinteger\fR\fR \fB\-osize\ \fR\fB\fIinteger\fR\fR \fB\-minsize\ \fR\fB\fIinteger\fR\fR \fB\-maxsize\ \fR\fB\fIinteger\fR\fR \fB\-otm\ \fR\fB\fIfloat\fR\fR \fB\-mintm\ \fR\fB\fIfloat\fR\fR \fB\-maxtm\ \fR\fB\fIfloat\fR\fR \fB\-maxdifftm\ \fR\fB\fIfloat\fR\fR \fB\-ogcpercent\ \fR\fB\fIfloat\fR\fR \fB\-mingc\ \fR\fB\fIfloat\fR\fR \fB\-maxgc\ \fR\fB\fIfloat\fR\fR \fB\-saltconc\ \fR\fB\fIfloat\fR\fR \fB\-dnaconc\ \fR\fB\fIfloat\fR\fR \fB\-maxpolyx\ \fR\fB\fIinteger\fR\fR \fB\-psizeopt\ \fR\fB\fIinteger\fR\fR \fB\-prange\ \fR\fB\fIrange\fR\fR \fB\-ptmopt\ \fR\fB\fIfloat\fR\fR \fB\-ptmmin\ \fR\fB\fIfloat\fR\fR \fB\-ptmmax\ \fR\fB\fIfloat\fR\fR \fB\-oexcludedregion\ \fR\fB\fIrange\fR\fR \fB\-oligoinput\ \fR\fB\fIstring\fR\fR \fB\-osizeopt\ \fR\fB\fIinteger\fR\fR \fB\-ominsize\ \fR\fB\fIinteger\fR\fR \fB\-omaxsize\ \fR\fB\fIinteger\fR\fR \fB\-otmopt\ \fR\fB\fIfloat\fR\fR \fB\-otmmin\ \fR\fB\fIfloat\fR\fR \fB\-otmmax\ \fR\fB\fIfloat\fR\fR \fB\-ogcopt\ \fR\fB\fIfloat\fR\fR \fB\-ogcmin\ \fR\fB\fIfloat\fR\fR \fB\-ogcmax\ \fR\fB\fIfloat\fR\fR \fB\-osaltconc\ \fR\fB\fIfloat\fR\fR \fB\-odnaconc\ \fR\fB\fIfloat\fR\fR \fB\-oanyself\ \fR\fB\fIfloat\fR\fR \fB\-oendself\ \fR\fB\fIfloat\fR\fR \fB\-opolyxmax\ \fR\fB\fIinteger\fR\fR \fB\-omishybmax\ \fR\fB\fIfloat\fR\fR \fB\-explainflag\ \fR\fB\fIboolean\fR\fR \fB\-fileflag\ \fR\fB\fIboolean\fR\fR \fB\-firstbaseindex\ \fR\fB\fIinteger\fR\fR \fB\-pickanyway\ \fR\fB\fIboolean\fR\fR \fB\-maxmispriming\ \fR\fB\fIfloat\fR\fR \fB\-pairmaxmispriming\ \fR\fB\fIfloat\fR\fR \fB\-numnsaccepted\ \fR\fB\fIinteger\fR\fR \fB\-selfany\ \fR\fB\fIfloat\fR\fR \fB\-selfend\ \fR\fB\fIfloat\fR\fR \fB\-scorrection\ \fR\fB\fIlist\fR\fR \fB\-tmformula\ \fR\fB\fIlist\fR\fR \fB\-maxendstability\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBeprimer32\fR\ 'u \fBeprimer32\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBeprimer32\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Primers" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 The sequence from which to choose primers\&. The sequence must be presented 5\*(Aq to 3\*(Aq .RE .PP \fB\-primer\fR \fItoggle\fR .RS 4 Tell Eprimer32 to pick primer(s) Default value: Y .RE .PP \fB\-task\fR \fIlist\fR .RS 4 Tell Eprimer32 what task to perform\&. Legal values are 1: \*(AqPick PCR primers\*(Aq, 2: \*(AqPick forward primer only\*(Aq, 3: \*(AqPick reverse primer only\*(Aq, 4: \*(AqNo primers needed\*(Aq\&. Default value: 1 .RE .PP \fB\-hybridprobe\fR \fItoggle\fR .RS 4 An \*(Aqinternal oligo\*(Aq is intended to be used as a hybridization probe (hyb probe) to detect the PCR product after amplification\&. Default value: N .RE .PP \fB\-mishyblibraryfile\fR \fIinfile\fR .RS 4 Similar to MISPRIMING\-LIBRARY, except that the event we seek to avoid is hybridization of the internal oligo to sequences in this library rather than priming from them\&. The file must be in (a slightly restricted) FASTA format (W\&. B\&. Pearson and D\&.J\&. Lipman, PNAS 85:8 pp 2444\-2448 [1988]); we briefly discuss the organization of this file below\&. If this parameter is specified then Eprimer32 locally aligns each candidate oligo against each library sequence and rejects those primers for which the local alignment score times a specified weight (see below) exceeds INTERNAL\-OLIGO\-MAX\-MISHYB\&. (The maximum value of the weight is arbitrarily set to 12\&.0\&.) Each sequence entry in the FASTA\-format file must begin with an \*(Aqid line\*(Aq that starts with \*(Aq>\*(Aq\&. The contents of the id line is \*(Aqslightly restricted\*(Aq in that Eprimer32 parses everything after any optional asterisk (\*(Aq*\*(Aq) as a floating point number to use as the weight mentioned above\&. If the id line contains no asterisk then the weight defaults to 1\&.0\&. The alignment scoring system used is the same as for calculating complementarity among oligos (e\&.g\&. SELF\-ANY)\&. The remainder of an entry contains the sequence as lines following the id line up until a line starting with \*(Aq>\*(Aq or the end of the file\&. Whitespace and newlines are ignored\&. Characters \*(AqA\*(Aq, \*(AqT\*(Aq, \*(AqG\*(Aq, \*(AqC\*(Aq, \*(Aqa\*(Aq, \*(Aqt\*(Aq, \*(Aqg\*(Aq, \*(Aqc\*(Aq are retained and any other character is converted to \*(AqN\*(Aq (with the consequence that any IUB / IUPAC codes for ambiguous bases are converted to \*(AqN\*(Aq)\&. There are no restrictions on line length\&. An empty value for this parameter indicates that no library should be used\&. .RE .PP \fB\-mispriminglibraryfile\fR \fIinfile\fR .RS 4 The name of a file containing a nucleotide sequence library of sequences to avoid amplifying (for example repetitive sequences, or possibly the sequences of genes in a gene family that should not be amplified\&.) The file must be in (a slightly restricted) FASTA format (W\&. B\&. Pearson and D\&.J\&. Lipman, PNAS 85:8 pp 2444\-2448 [1988]); we briefly discuss the organization of this file below\&. If this parameter is specified then Eprimer32 locally aligns each candidate primer against each library sequence and rejects those primers for which the local alignment score times a specified weight (see below) exceeds MAX\-MISPRIMING\&. (The maximum value of the weight is arbitrarily set to 100\&.0\&.) Each sequence entry in the FASTA\-format file must begin with an \*(Aqid line\*(Aq that starts with \*(Aq>\*(Aq\&. The contents of the id line is \*(Aqslightly restricted\*(Aq in that Eprimer32 parses everything after any optional asterisk (\*(Aq*\*(Aq) as a floating point number to use as the weight mentioned above\&. If the id line contains no asterisk then the weight defaults to 1\&.0\&. The alignment scoring system used is the same as for calculating complementarity among oligos (e\&.g\&. SELF\-ANY)\&. The remainder of an entry contains the sequence as lines following the id line up until a line starting with \*(Aq>\*(Aq or the end of the file\&. Whitespace and newlines are ignored\&. Characters \*(AqA\*(Aq, \*(AqT\*(Aq, \*(AqG\*(Aq, \*(AqC\*(Aq, \*(Aqa\*(Aq, \*(Aqt\*(Aq, \*(Aqg\*(Aq, \*(Aqc\*(Aq are retained and any other character is converted to \*(AqN\*(Aq (with the consequence that any IUB / IUPAC codes for ambiguous bases are converted to \*(AqN\*(Aq)\&. There are no restrictions on line length\&. An empty value for this parameter indicates that no repeat library should be used\&. .RE .SS "Additional section" .SS "Program options" .PP \fB\-numreturn\fR \fIinteger\fR .RS 4 The maximum number of primer pairs to return\&. Primer pairs returned are sorted by their \*(Aqquality\*(Aq, in other words by the value of the objective function (where a lower number indicates a better primer pair)\&. Caution: setting this parameter to a large value will increase running time\&. Default value: 5 .RE .SS "Sequence options" .PP \fB\-includedregion\fR \fIrange\fR .RS 4 A sub\-region of the given sequence in which to pick primers\&. For example, often the first dozen or so bases of a sequence are vector, and should be excluded from consideration\&. The value for this parameter has the form (start),(end) where (start) is the index of the first base to consider, and (end) is the last in the primer\-picking region\&. .RE .PP \fB\-targetregion\fR \fIrange\fR .RS 4 If one or more Targets is specified then a legal primer pair must flank at least one of them\&. A Target might be a simple sequence repeat site (for example a CA repeat) or a single\-base\-pair polymorphism\&. The value should be a space\-separated list of (start),(end) pairs where (start) is the index of the first base of a Target, and (end) is the last E\&.g\&. 50,51 requires primers to surround the 2 bases at positions 50 and 51\&. .RE .PP \fB\-excludedregion\fR \fIrange\fR .RS 4 Primer oligos may not overlap any region specified in this tag\&. The associated value must be a space\-separated list of (start),(end) pairs where (start) is the index of the first base of the excluded region, and and (end) is the last\&. This tag is useful for tasks such as excluding regions of low sequence quality or for excluding regions containing repetitive elements such as ALUs or LINEs\&. E\&.g\&. 401,407 68,70 forbids selection of primers in the 7 bases starting at 401 and the 3 bases at 68\&. .RE .PP \fB\-forwardinput\fR \fIstring\fR .RS 4 The sequence of a forward primer to check and around which to design reverse primers and optional internal oligos\&. Must be a substring of SEQUENCE\&. .RE .PP \fB\-reverseinput\fR \fIstring\fR .RS 4 The sequence of a reverse primer to check and around which to design forward primers and optional internal oligos\&. Must be a substring of the reverse strand of SEQUENCE\&. .RE .SS "Primer options" .PP \fB\-gcclamp\fR \fIinteger\fR .RS 4 Require the specified number of consecutive Gs and Cs at the 3\*(Aq end of both the forward and reverse primer\&. (This parameter has no effect on the internal oligo if one is requested\&.) .RE .PP \fB\-osize\fR \fIinteger\fR .RS 4 Optimum length (in bases) of a primer oligo\&. Eprimer32 will attempt to pick primers close to this length\&. Default value: 20 .RE .PP \fB\-minsize\fR \fIinteger\fR .RS 4 Minimum acceptable length of a primer\&. Must be greater than 0 and less than or equal to MAX\-SIZE\&. Default value: 18 .RE .PP \fB\-maxsize\fR \fIinteger\fR .RS 4 Maximum acceptable length (in bases) of a primer\&. Currently this parameter cannot be larger than 35\&. This limit is governed by the maximum oligo size for which Eprimer32\*(Aqs melting\-temperature is valid\&. Default value: 27 .RE .PP \fB\-otm\fR \fIfloat\fR .RS 4 Optimum melting temperature(Celsius) for a primer oligo\&. Eprimer32 will try to pick primers with melting temperatures are close to this temperature\&. The oligo melting temperature formula in Eprimer32 is that given in Rychlik, Spencer and Rhoads, Nucleic Acids Research, vol 18, num 21, pp 6409\-6412 and Breslauer, Frank, Bloecker and Marky, Proc\&. Natl\&. Acad\&. Sci\&. USA, vol 83, pp 3746\-3750\&. Please refer to the former paper for background discussion\&. Default value: 60\&.0 .RE .PP \fB\-mintm\fR \fIfloat\fR .RS 4 Minimum acceptable melting temperature(Celsius) for a primer oligo\&. Default value: 57\&.0 .RE .PP \fB\-maxtm\fR \fIfloat\fR .RS 4 Maximum acceptable melting temperature(Celsius) for a primer oligo\&. Default value: 63\&.0 .RE .PP \fB\-maxdifftm\fR \fIfloat\fR .RS 4 Maximum acceptable (unsigned) difference between the melting temperatures of the forward and reverse primers\&. Default value: 100\&.0 .RE .PP \fB\-ogcpercent\fR \fIfloat\fR .RS 4 Primer optimum GC percent\&. Default value: 50\&.0 .RE .PP \fB\-mingc\fR \fIfloat\fR .RS 4 Minimum allowable percentage of Gs and Cs in any primer\&. Default value: 20\&.0 .RE .PP \fB\-maxgc\fR \fIfloat\fR .RS 4 Maximum allowable percentage of Gs and Cs in any primer generated by Primer\&. Default value: 80\&.0 .RE .PP \fB\-saltconc\fR \fIfloat\fR .RS 4 The millimolar concentration of salt (usually KCl) in the PCR\&. Eprimer32 uses this argument to calculate oligo melting temperatures\&. Default value: 50\&.0 .RE .PP \fB\-dnaconc\fR \fIfloat\fR .RS 4 The nanomolar concentration of annealing oligos in the PCR\&. Eprimer32 uses this argument to calculate oligo melting temperatures\&. The default (50nM) works well with the standard protocol used at the Whitehead/MIT Center for Genome Research\-\-0\&.5 microliters of 20 micromolar concentration for each primer oligo in a 20 microliter reaction with 10 nanograms template, 0\&.025 units/microliter Taq polymerase in 0\&.1 mM each dNTP, 1\&.5mM MgCl2, 50mM KCl, 10mM Tris\-HCL (pH 9\&.3) using 35 cycles with an annealing temperature of 56 degrees Celsius\&. This parameter corresponds to \*(Aqc\*(Aq in Rychlik, Spencer and Rhoads\*(Aq equation (ii) (Nucleic Acids Research, vol 18, num 21) where a suitable value (for a lower initial concentration of template) is \*(Aqempirically determined\*(Aq\&. The value of this parameter is less than the actual concentration of oligos in the reaction because it is the concentration of annealing oligos, which in turn depends on the amount of template (including PCR product) in a given cycle\&. This concentration increases a great deal during a PCR; fortunately PCR seems quite robust for a variety of oligo melting temperatures\&. See ADVICE FOR PICKING PRIMERS\&. Default value: 50\&.0 .RE .PP \fB\-maxpolyx\fR \fIinteger\fR .RS 4 The maximum allowable length of a mononucleotide repeat in a primer, for example AAAAAA\&. Default value: 5 .RE .SS "Product options" .PP \fB\-psizeopt\fR \fIinteger\fR .RS 4 The optimum size for the PCR product\&. 0 indicates that there is no optimum product size\&. Default value: 200 .RE .PP \fB\-prange\fR \fIrange\fR .RS 4 The associated values specify the lengths of the product that the user wants the primers to create, and is a space separated list of elements of the form (x)\-(y) where an (x)\-(y) pair is a legal range of lengths for the product\&. For example, if one wants PCR products to be between 100 to 150 bases (inclusive) then one would set this parameter to 100\-150\&. If one desires PCR products in either the range from 100 to 150 bases or in the range from 200 to 250 bases then one would set this parameter to 100\-150 200\-250\&. Eprimer32 favours ranges to the left side of the parameter string\&. Eprimer32 will return legal primers pairs in the first range regardless the value of the objective function for these pairs\&. Only if there are an insufficient number of primers in the first range will Eprimer32 return primers in a subsequent range\&. Default value: 100\-300 .RE .PP \fB\-ptmopt\fR \fIfloat\fR .RS 4 The optimum melting temperature for the PCR product\&. 0 indicates that there is no optimum temperature\&. Default value: 0\&.0 .RE .PP \fB\-ptmmin\fR \fIfloat\fR .RS 4 The minimum allowed melting temperature of the amplicon\&. Please see the documentation on the maximum melting temperature of the product for details\&. Default value: \-1000000\&.0 .RE .PP \fB\-ptmmax\fR \fIfloat\fR .RS 4 The maximum allowed melting temperature of the amplicon\&. Product Tm is calculated using the formula from Bolton and McCarthy, PNAS 84:1390 (1962) as presented in Sambrook, Fritsch and Maniatis, Molecular Cloning, p 11\&.46 (1989, CSHL Press)\&. Tm = 81\&.5 + 16\&.6(log10([Na+])) + \&.41*(%GC) \- 600/length Where [Na+} is the molar sodium concentration, (%GC) is the percent of Gs and Cs in the sequence, and length is the length of the sequence\&. A similar formula is used by the prime primer selection program in GCG, which instead uses 675\&.0/length in the last term (after F\&. Baldino, Jr, M\&.\-F\&. Chesselet, and M\&.E\&. Lewis, Methods in Enzymology 168:766 (1989) eqn (1) on page 766 without the mismatch and formamide terms)\&. The formulas here and in Baldino et al\&. assume Na+ rather than K+\&. According to J\&.G\&. Wetmur, Critical Reviews in BioChem\&. and Mol\&. Bio\&. 26:227 (1991) 50 mM K+ should be equivalent in these formulae to \&.2 M Na+\&. Eprimer32 uses the same salt concentration value for calculating both the primer melting temperature and the oligo melting temperature\&. If you are planning to use the PCR product for hybridization later this behavior will not give you the Tm under hybridization conditions\&. Default value: 1000000\&.0 .RE .SS "Internal oligo input" .PP \fB\-oexcludedregion\fR \fIrange\fR .RS 4 Middle oligos may not overlap any region specified by this tag\&. The associated value must be a space\-separated list of (start),(end) pairs, where (start) is the index of the first base of an excluded region, and (end) is the last\&. Often one would make Target regions excluded regions for internal oligos\&. .RE .PP \fB\-oligoinput\fR \fIstring\fR .RS 4 The sequence of an internal oligo to check and around which to design forward and reverse primers\&. Must be a substring of SEQUENCE\&. .RE .SS "Internal oligo options" .PP \fB\-osizeopt\fR \fIinteger\fR .RS 4 Optimum length (in bases) of an internal oligo\&. Eprimer32 will attempt to pick primers close to this length\&. Default value: 20 .RE .PP \fB\-ominsize\fR \fIinteger\fR .RS 4 Minimum acceptable length of an internal oligo\&. Must be greater than 0 and less than or equal to INTERNAL\-OLIGO\-MAX\-SIZE\&. Default value: 18 .RE .PP \fB\-omaxsize\fR \fIinteger\fR .RS 4 Maximum acceptable length (in bases) of an internal oligo\&. Currently this parameter cannot be larger than 35\&. This limit is governed by maximum oligo size for which Eprimer32\*(Aqs melting\-temperature is valid\&. Default value: 27 .RE .PP \fB\-otmopt\fR \fIfloat\fR .RS 4 Optimum melting temperature (Celsius) for an internal oligo\&. Eprimer32 will try to pick oligos with melting temperatures that are close to this temperature\&. The oligo melting temperature formula in Eprimer32 is that given in Rychlik, Spencer and Rhoads, Nucleic Acids Research, vol 18, num 21, pp 6409\-6412 and Breslauer, Frank, Bloecker and Marky, Proc\&. Natl\&. Acad\&. Sci\&. USA, vol 83, pp 3746\-3750\&. Please refer to the former paper for background discussion\&. Default value: 60\&.0 .RE .PP \fB\-otmmin\fR \fIfloat\fR .RS 4 Minimum acceptable melting temperature(Celsius) for an internal oligo\&. Default value: 57\&.0 .RE .PP \fB\-otmmax\fR \fIfloat\fR .RS 4 Maximum acceptable melting temperature (Celsius) for an internal oligo\&. Default value: 63\&.0 .RE .PP \fB\-ogcopt\fR \fIfloat\fR .RS 4 Internal oligo optimum GC percent\&. Default value: 50\&.0 .RE .PP \fB\-ogcmin\fR \fIfloat\fR .RS 4 Minimum allowable percentage of Gs and Cs in an internal oligo\&. Default value: 20\&.0 .RE .PP \fB\-ogcmax\fR \fIfloat\fR .RS 4 Maximum allowable percentage of Gs and Cs in any internal oligo generated by Primer\&. Default value: 80\&.0 .RE .PP \fB\-osaltconc\fR \fIfloat\fR .RS 4 The millimolar concentration of salt (usually KCl) in the hybridization\&. Eprimer32 uses this argument to calculate internal oligo melting temperatures\&. Default value: 50\&.0 .RE .PP \fB\-odnaconc\fR \fIfloat\fR .RS 4 The nanomolar concentration of annealing internal oligo in the hybridization\&. Default value: 50\&.0 .RE .PP \fB\-oanyself\fR \fIfloat\fR .RS 4 The maximum allowable local alignment score when testing an internal oligo for (local) self\-complementarity\&. Local self\-complementarity is taken to predict the tendency of oligos to anneal to themselves The scoring system gives 1\&.00 for complementary bases, \-0\&.25 for a match of any base (or N) with an N, \-1\&.00 for a mismatch, and \-2\&.00 for a gap\&. Only single\-base\-pair gaps are allowed\&. For example, the alignment 5\*(Aq ATCGNA 3\*(Aq || | | 3\*(Aq TA\-CGT 5\*(Aq is allowed (and yields a score of 1\&.75), but the alignment 5\*(Aq ATCCGNA 3\*(Aq || | | 3\*(Aq TA\-\-CGT 5\*(Aq is not considered\&. Scores are non\-negative, and a score of 0\&.00 indicates that there is no reasonable local alignment between two oligos\&. Default value: 12\&.00 .RE .PP \fB\-oendself\fR \fIfloat\fR .RS 4 The maximum allowable 3\*(Aq\-anchored global alignment score when testing a single oligo for self\-complementarity\&. The scoring system is as for the Maximum Complementarity argument\&. In the examples above the scores are 7\&.00 and 6\&.00 respectively\&. Scores are non\-negative, and a score of 0\&.00 indicates that there is no reasonable 3\*(Aq\-anchored global alignment between two oligos\&. In order to estimate 3\*(Aq\-anchored global alignments for candidate oligos, Primer assumes that the sequence from which to choose oligos is presented 5\*(Aq to 3\*(Aq\&. INTERNAL\-OLIGO\-SELF\-END is meaningless when applied to internal oligos used for hybridization\-based detection, since primer\-dimer will not occur\&. We recommend that INTERNAL\-OLIGO\-SELF\-END be set at least as high as INTERNAL\-OLIGO\-SELF\-ANY\&. Default value: 12\&.00 .RE .PP \fB\-opolyxmax\fR \fIinteger\fR .RS 4 The maximum allowable length of an internal oligo mononucleotide repeat, for example AAAAAA\&. Default value: 5 .RE .PP \fB\-omishybmax\fR \fIfloat\fR .RS 4 Similar to MAX\-MISPRIMING except that this parameter applies to the similarity of candidate internal oligos to the library specified in INTERNAL\-OLIGO\-MISHYB\-LIBRARY\&. Default value: 12\&.0 .RE .SS "Advanced section" .PP \fB\-explainflag\fR \fIboolean\fR .RS 4 If this flag is true, produce LEFT\-EXPLAIN, RIGHT\-EXPLAIN, and INTERNAL\-OLIGO\-EXPLAIN output tags, which are intended to provide information on the number of oligos and primer pairs that Eprimer32 examined, and statistics on the number discarded for various reasons\&. Default value: N .RE .PP \fB\-fileflag\fR \fIboolean\fR .RS 4 If the associated value is true, then Eprimer32 creates two output files for each input SEQUENCE\&. File (sequence\-id)\&.for lists all acceptable forward primers for (sequence\-id), and (sequence\-id)\&.rev lists all acceptable reverse primers for (sequence\-id), where (sequence\-id) is the value of the SEQUENCE\-ID tag (which must be supplied)\&. In addition, if the input tag TASK is 1 or 4, Eprimer32 produces a file (sequence\-id)\&.int, which lists all acceptable internal oligos\&. Default value: N .RE .PP \fB\-firstbaseindex\fR \fIinteger\fR .RS 4 This parameter is the index of the first base in the input sequence\&. For input and output using 1\-based indexing (such as that used in GenBank and to which many users are accustomed) set this parameter to 1\&. For input and output using 0\-based indexing set this parameter to 0\&. (This parameter also affects the indexes in the contents of the files produced when the primer file flag is set\&.) Default value: 1 .RE .PP \fB\-pickanyway\fR \fIboolean\fR .RS 4 If true pick a primer pair even if LEFT\-INPUT, RIGHT\-INPUT, or INTERNAL\-OLIGO\-INPUT violates specific constraints\&. Default value: N .RE .PP \fB\-maxmispriming\fR \fIfloat\fR .RS 4 The maximum allowed weighted similarity with any sequence in MISPRIMING\-LIBRARY\&. Default value: 12\&.00 .RE .PP \fB\-pairmaxmispriming\fR \fIfloat\fR .RS 4 The maximum allowed sum of weighted similarities of a primer pair (one similarity for each primer) with any single sequence in MISPRIMING\-LIBRARY\&. Default value: 24\&.00 .RE .PP \fB\-numnsaccepted\fR \fIinteger\fR .RS 4 Maximum number of unknown bases (N) allowable in any primer\&. .RE .PP \fB\-selfany\fR \fIfloat\fR .RS 4 The maximum allowable local alignment score when testing a single primer for (local) self\-complementarity and the maximum allowable local alignment score when testing for complementarity between forward and reverse primers\&. Local self\-complementarity is taken to predict the tendency of primers to anneal to each other without necessarily causing self\-priming in the PCR\&. The scoring system gives 1\&.00 for complementary bases, \-0\&.25 for a match of any base (or N) with an N, \-1\&.00 for a mismatch, and \-2\&.00 for a gap\&. Only single\-base\-pair gaps are allowed\&. For example, the alignment 5\*(Aq ATCGNA 3\*(Aq \&.\&.\&.|| | | 3\*(Aq TA\-CGT 5\*(Aq is allowed (and yields a score of 1\&.75), but the alignment 5\*(Aq ATCCGNA 3\*(Aq \&.\&.\&.|| | | 3\*(Aq TA\-\-CGT 5\*(Aq is not considered\&. Scores are non\-negative, and a score of 0\&.00 indicates that there is no reasonable local alignment between two oligos\&. Default value: 8\&.00 .RE .PP \fB\-selfend\fR \fIfloat\fR .RS 4 The maximum allowable 3\*(Aq\-anchored global alignment score when testing a single primer for self\-complementarity, and the maximum allowable 3\*(Aq\-anchored global alignment score when testing for complementarity between forward and reverse primers\&. The 3\*(Aq\-anchored global alignment score is taken to predict the likelihood of PCR\-priming primer\-dimers, for example 5\*(Aq ATGCCCTAGCTTCCGGATG 3\*(Aq \&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.||| ||||| \&.\&.\&.\&.\&.\&.\&.\&.\&.\&.3\*(Aq AAGTCCTACATTTAGCCTAGT 5\*(Aq or 5\*(Aq AGGCTATGGGCCTCGCGA 3\*(Aq \&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.|||||| \&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.\&.3\*(Aq AGCGCTCCGGGTATCGGA 5\*(Aq The scoring system is as for the Maximum Complementarity argument\&. In the examples above the scores are 7\&.00 and 6\&.00 respectively\&. Scores are non\-negative, and a score of 0\&.00 indicates that there is no reasonable 3\*(Aq\-anchored global alignment between two oligos\&. In order to estimate 3\*(Aq\-anchored global alignments for candidate primers and primer pairs, Primer assumes that the sequence from which to choose primers is presented 5\*(Aq to 3\*(Aq\&. It is nonsensical to provide a larger value for this parameter than for the Maximum (local) Complementarity parameter because the score of a local alignment will always be at least as great as the score of a global alignment\&. Default value: 3\&.00 .RE .PP \fB\-scorrection\fR \fIlist\fR .RS 4 Specifies the salt correction formula for the melting temperature calculation\&. Default value: 1 .RE .PP \fB\-tmformula\fR \fIlist\fR .RS 4 Specifies details of melting temperature calculation\&. Default value: 1 .RE .SS "Primer penalty weights" .PP \fB\-maxendstability\fR \fIfloat\fR .RS 4 The maximum stability for the five 3\*(Aq bases of a forward or reverse primer\&. Bigger numbers mean more stable 3\*(Aq ends\&. The value is the maximum delta G for duplex disruption for the five 3\*(Aq bases as calculated using the nearest neighbor parameters published in Breslauer, Frank, Bloecker and Marky, Proc\&. Natl\&. Acad\&. Sci\&. USA, vol 83, pp 3746\-3750\&. Eprimer32 uses a completely permissive default value for backward compatibility (which we may change in the next release)\&. Rychlik recommends a maximum value of 9 (Wojciech Rychlik, \*(AqSelection of Primers for Polymerase Chain Reaction\*(Aq in BA White, Ed\&., \*(AqMethods in Molecular Biology, Vol\&. 15: PCR Protocols: Current Methods and Applications\*(Aq, 1993, pp 31\-40, Humana Press, Totowa NJ)\&. Default value: 9\&.0 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP eprimer32 is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/emowse.1e0000644000000000000000000000655212214054043012512 0ustar '\" t .\" Title: EMOWSE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "EMOWSE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" emowse \- Search protein sequences by digest fragment molecular weight .SH "SYNOPSIS" .HP \w'\fBemowse\fR\ 'u \fBemowse\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-mwdata\ \fR\fB\fIdatafile\fR\fR \fB\-frequencies\ \fR\fB\fIdatafile\fR\fR \fB\-weight\ \fR\fB\fIinteger\fR\fR \fB\-mono\ \fR\fB\fIboolean\fR\fR \fB\-enzyme\ \fR\fB\fIlist\fR\fR \fB\-pcrange\ \fR\fB\fIinteger\fR\fR \fB\-tolerance\ \fR\fB\fIfloat\fR\fR \fB\-partials\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBemowse\fR\ 'u \fBemowse\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBemowse\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Composition" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .PP \fB\-mwdata\fR \fIdatafile\fR .RS 4 Default value: Emolwt\&.dat .RE .PP \fB\-frequencies\fR \fIdatafile\fR .RS 4 Default value: Efreqs\&.dat .RE .SS "Required section" .PP \fB\-weight\fR \fIinteger\fR .RS 4 .RE .PP \fB\-mono\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Advanced section" .PP \fB\-enzyme\fR \fIlist\fR .RS 4 Default value: 1 .RE .PP \fB\-pcrange\fR \fIinteger\fR .RS 4 Default value: 25 .RE .PP \fB\-tolerance\fR \fIfloat\fR .RS 4 Default value: 0\&.1 .RE .PP \fB\-partials\fR \fIfloat\fR .RS 4 Default value: 0\&.4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP emowse is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/aligncopy.1e0000644000000000000000000000564012214054043013175 0ustar '\" t .\" Title: ALIGNCOPY .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ALIGNCOPY" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" aligncopy \- Reads and writes alignments .SH "SYNOPSIS" .HP \w'\fBaligncopy\fR\ 'u \fBaligncopy\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR [\fB\-name\ \fR\fB\fIstring\fR\fR] [\fB\-comment\ \fR\fB\fIstring\fR\fR] [\fB\-append\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIalign\fR\fR .HP \w'\fBaligncopy\fR\ 'u \fBaligncopy\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBaligncopy\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequences\fR \fIseqset\fR .RS 4 File containing a sequence alignment\&. .RE .SS "Required section" .SS "Additional section" .PP \fB\-name\fR \fIstring\fR .RS 4 .RE .PP \fB\-comment\fR \fIstring\fR .RS 4 .RE .PP \fB\-append\fR \fIboolean\fR .RS 4 This allows you to append the name and comments you have given on to the end of the existing alignment header\&. Default value: N .RE .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIalign\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP aligncopy is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/union.1e0000644000000000000000000000552412214054043012341 0ustar '\" t .\" Title: UNION .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "UNION" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" union \- Concatenate multiple sequences into a single sequence .SH "SYNOPSIS" .HP \w'\fBunion\fR\ 'u \fBunion\fR \fB\-feature\ \fR\fB\fIboolean\fR\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-source\ \fR\fB\fIboolean\fR\fR \fB\-findoverlap\ \fR\fB\fIboolean\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR [\fB\-overlapfile\ \fR\fB\fIoutfile\fR\fR] .HP \w'\fBunion\fR\ 'u \fBunion\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBunion\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-feature\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Advanced section" .PP \fB\-source\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-findoverlap\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqout\fR .RS 4 .RE .PP \fB\-overlapfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP union is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/domtesta.1e0000644000000000000000000000472112214054043013027 0ustar '\" t .\" Title: DOMTESTA .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DOMTESTA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" domtesta \- Reads an XML file into the DOM and writes it back out .SH "SYNOPSIS" .HP \w'\fBdomtesta\fR\ 'u \fBdomtesta\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBdomtesta\fR\ 'u \fBdomtesta\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdomtesta\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP domtesta is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/infoalign.1e0000644000000000000000000001363712214054043013163 0ustar '\" t .\" Title: INFOALIGN .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "INFOALIGN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" infoalign \- Display basic information about a multiple sequence alignment .SH "SYNOPSIS" .HP \w'\fBinfoalign\fR\ 'u \fBinfoalign\fR \fB\-sequence\ \fR\fB\fIseqset\fR\fR [\fB\-matrix\ \fR\fB\fImatrix\fR\fR] [\fB\-refseq\ \fR\fB\fIstring\fR\fR] \fB\-plurality\ \fR\fB\fIfloat\fR\fR \fB\-identity\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR [\fB\-html\ \fR\fB\fIboolean\fR\fR] \fB\-only\ \fR\fB\fIboolean\fR\fR \fB\-heading\ \fR\fB\fIboolean\fR\fR \fB\-usa\ \fR\fB\fIboolean\fR\fR \fB\-name\ \fR\fB\fIboolean\fR\fR \fB\-seqlength\ \fR\fB\fIboolean\fR\fR \fB\-alignlength\ \fR\fB\fIboolean\fR\fR \fB\-gaps\ \fR\fB\fIboolean\fR\fR \fB\-gapcount\ \fR\fB\fIboolean\fR\fR \fB\-idcount\ \fR\fB\fIboolean\fR\fR \fB\-simcount\ \fR\fB\fIboolean\fR\fR \fB\-diffcount\ \fR\fB\fIboolean\fR\fR \fB\-change\ \fR\fB\fIboolean\fR\fR \fB\-weight\ \fR\fB\fIboolean\fR\fR \fB\-description\ \fR\fB\fIboolean\fR\fR .HP \w'\fBinfoalign\fR\ 'u \fBinfoalign\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBinfoalign\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Multiple,Data retrieval:Sequence data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqset\fR .RS 4 The sequence alignment to be displayed\&. .RE .PP \fB\-matrix\fR \fImatrix\fR .RS 4 This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&. .RE .PP \fB\-refseq\fR \fIstring\fR .RS 4 If you give the number in the alignment or the name of a sequence, it will be taken to be the reference sequence\&. The reference sequence is the one against which all the other sequences are compared\&. If this is set to 0 then the consensus sequence will be used as the reference sequence\&. By default the consensus sequence is used as the reference sequence\&. .RE .SS "Advanced section" .PP \fB\-plurality\fR \fIfloat\fR .RS 4 Set a cut\-off for the % of positive scoring matches below which there is no consensus\&. The default plurality is taken as 50% of the total weight of all the sequences in the alignment\&. Default value: 50\&.0 .RE .PP \fB\-identity\fR \fIfloat\fR .RS 4 Provides the facility of setting the required number of identities at a position for it to give a consensus\&. Therefore, if this is set to 100% only columns of identities contribute to the consensus\&. Default value: 0\&.0 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 If you enter the name of a file here then this program will write the sequence details into that file\&. .RE .PP \fB\-html\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-only\fR \fIboolean\fR .RS 4 This is a way of shortening the command line if you only want a few things to be displayed\&. Instead of specifying: \*(Aq\-nohead \-nousa \-noname \-noalign \-nogaps \-nogapcount \-nosimcount \-noidcount \-nodiffcount \-noweight\*(Aq to get only the sequence length output, you can specify \*(Aq\-only \-seqlength\*(Aq Default value: N .RE .PP \fB\-heading\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-usa\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-name\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-seqlength\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-alignlength\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-gaps\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-gapcount\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-idcount\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-simcount\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-diffcount\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-change\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-weight\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .PP \fB\-description\fR \fIboolean\fR .RS 4 Default value: @(!$(only)) .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP infoalign is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/edamisformat.1e0000644000000000000000000000700212214054043013655 0ustar '\" t .\" Title: EDAMISFORMAT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "EDAMISFORMAT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" edamisformat \- Find EDAM ontology terms by is_format_of relation .SH "SYNOPSIS" .HP \w'\fBedamisformat\fR\ 'u \fBedamisformat\fR \fB\-identifier\ \fR\fB\fIstring\fR\fR [\fB\-namespace\ \fR\fB\fIlist\fR\fR] \fB\-sensitive\ \fR\fB\fIboolean\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-edamisformat\ \fR\fB\fIoutobo\fR\fR .HP \w'\fBedamisformat\fR\ 'u \fBedamisformat\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBedamisformat\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Data retrieval:Ontology data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-identifier\fR \fIstring\fR .RS 4 .RE .SS "Additional section" .PP \fB\-namespace\fR \fIlist\fR .RS 4 By default all terms are returned\&. Searches can be limited to one or a few namespaces\&. Default value: * .RE .SS "Advanced section" .PP \fB\-sensitive\fR \fIboolean\fR .RS 4 By default, the query keywords are matched against the EDAM term names (and synonyms) only\&. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches\&. Default value: N .RE .PP \fB\-subclasses\fR \fIboolean\fR .RS 4 Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: N .RE .PP \fB\-obsolete\fR \fIboolean\fR .RS 4 The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N .RE .SS "Output section" .PP \fB\-edamisformat\fR \fIoutobo\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP edamisformat is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/goseq.1e0000644000000000000000000000535712214054043012333 0ustar '\" t .\" Title: GOSEQ .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "GOSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" goseq \- Identify sequence entries containing GO terms .SH "SYNOPSIS" .HP \w'\fBgoseq\fR\ 'u \fBgoseq\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-term\ \fR\fB\fIstring\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBgoseq\fR\ 'u \fBgoseq\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBgoseq\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-term\fR \fIstring\fR .RS 4 This is the name of a term from the GO ontology\&. If you are not sure what names are available, use ontoget\&. .RE .SS "Required section" .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 The list of sequence names will be written to this list file .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP goseq is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/notab.1e0000644000000000000000000000476612214054043012323 0ustar '\" t .\" Title: NOTAB .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "NOTAB" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" notab \- Replace tabs with spaces in an ASCII text file .SH "SYNOPSIS" .HP \w'\fBnotab\fR\ 'u \fBnotab\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBnotab\fR\ 'u \fBnotab\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBnotab\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .SS "Required section" .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP notab is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/wobble.1e0000644000000000000000000000543412214054043012463 0ustar '\" t .\" Title: WOBBLE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "WOBBLE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" wobble \- Plot third base position variability in a nucleotide sequence .SH "SYNOPSIS" .HP \w'\fBwobble\fR\ 'u \fBwobble\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR [\fB\-window\ \fR\fB\fIinteger\fR\fR] \fB\-bases\ \fR\fB\fIstring\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBwobble\fR\ 'u \fBwobble\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBwobble\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Gene finding" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .SS "Additional section" .PP \fB\-window\fR \fIinteger\fR .RS 4 Default value: 30 .RE .SS "Advanced section" .PP \fB\-bases\fR \fIstring\fR .RS 4 Default value: GC .RE .SS "Output section" .PP \fB\-graph\fR \fIxygraph\fR .RS 4 .RE .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP wobble is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/ontocount.1e0000644000000000000000000000565312214054043013244 0ustar '\" t .\" Title: ONTOCOUNT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ONTOCOUNT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" ontocount \- Count ontology term(s) .SH "SYNOPSIS" .HP \w'\fBontocount\fR\ 'u \fBontocount\fR \fB\-oboterms\ \fR\fB\fIobo\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-obsolete\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBontocount\fR\ 'u \fBontocount\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBontocount\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-oboterms\fR \fIobo\fR .RS 4 .RE .SS "Additional section" .SS "Advanced section" .PP \fB\-subclasses\fR \fIboolean\fR .RS 4 Extend the query matches to include all terms which are specialisations (sub\-classes) of the matched terms\&. Default value: N .RE .PP \fB\-obsolete\fR \fIboolean\fR .RS 4 The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP ontocount is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/seqretallfeat.1e0000644000000000000000000000477712214054043014056 0ustar '\" t .\" Title: SEQRETALLFEAT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SEQRETALLFEAT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" seqretallfeat \- Reads and writes (returns) one or more sequences .SH "SYNOPSIS" .HP \w'\fBseqretallfeat\fR\ 'u \fBseqretallfeat\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBseqretallfeat\fR\ 'u \fBseqretallfeat\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBseqretallfeat\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Test" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP seqretallfeat is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/geecee.1e0000644000000000000000000000472612214054043012431 0ustar '\" t .\" Title: GEECEE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "GEECEE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" geecee \- Calculate fractional GC content of nucleic acid sequences .SH "SYNOPSIS" .HP \w'\fBgeecee\fR\ 'u \fBgeecee\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBgeecee\fR\ 'u \fBgeecee\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBgeecee\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:CpG Islands" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP geecee is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/tfscan.1e0000644000000000000000000000555312214054043012471 0ustar '\" t .\" Title: TFSCAN .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "TFSCAN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" tfscan \- Identify transcription factor binding sites in DNA sequences .SH "SYNOPSIS" .HP \w'\fBtfscan\fR\ 'u \fBtfscan\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-menu\ \fR\fB\fIlist\fR\fR \fB\-custom\ \fR\fB\fIdatafile\fR\fR \fB\-mismatch\ \fR\fB\fIinteger\fR\fR [\fB\-minlength\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIreport\fR\fR .HP \w'\fBtfscan\fR\ 'u \fBtfscan\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBtfscan\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Transcription" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-menu\fR \fIlist\fR .RS 4 Default value: V .RE .PP \fB\-custom\fR \fIdatafile\fR .RS 4 .RE .SS "Required section" .PP \fB\-mismatch\fR \fIinteger\fR .RS 4 .RE .SS "Additional section" .PP \fB\-minlength\fR \fIinteger\fR .RS 4 Default value: 1 .RE .SS "Output section" .PP \fB\-outfile\fR \fIreport\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP tfscan is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/pepcoil.1e0000644000000000000000000000557412214054043012651 0ustar '\" t .\" Title: PEPCOIL .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PEPCOIL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" pepcoil \- Predicts coiled coil regions in protein sequences .SH "SYNOPSIS" .HP \w'\fBpepcoil\fR\ 'u \fBpepcoil\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-coil\ \fR\fB\fIboolean\fR\fR \fB\-frame\ \fR\fB\fIboolean\fR\fR \fB\-other\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR .HP \w'\fBpepcoil\fR\ 'u \fBpepcoil\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBpepcoil\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:2D Structure,Protein:Domains" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Required section" .PP \fB\-window\fR \fIinteger\fR .RS 4 Default value: 28 .RE .SS "Output section" .PP \fB\-coil\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-frame\fR \fIboolean\fR .RS 4 Default value: $(coil) .RE .PP \fB\-other\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-outfile\fR \fIreport\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP pepcoil is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/taxget.1e0000644000000000000000000000472312214054043012505 0ustar '\" t .\" Title: TAXGET .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "TAXGET" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" taxget \- Get taxon(s) .SH "SYNOPSIS" .HP \w'\fBtaxget\fR\ 'u \fBtaxget\fR \fB\-taxons\ \fR\fB\fItaxon\fR\fR \fB\-outfile\ \fR\fB\fIouttaxon\fR\fR .HP \w'\fBtaxget\fR\ 'u \fBtaxget\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBtaxget\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:Taxonomy" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-taxons\fR \fItaxon\fR .RS 4 .RE .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIouttaxon\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP taxget is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/ajtest.1e0000644000000000000000000000564112214054043012503 0ustar '\" t .\" Title: AJTEST .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "AJTEST" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" ajtest \- Test file for ACD parsing .SH "SYNOPSIS" .HP \w'\fBajtest\fR\ 'u \fBajtest\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-bsequence\ \fR\fB\fIseqset\fR\fR \fB\-idresource\ \fR\fB\fIstring\fR\fR \fB\-taxdir\ \fR\fB\fIdirectory\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR \fB\-outfeat\ \fR\fB\fIfeatout\fR\fR \fB\-outdir\ \fR\fB\fIoutdir\fR\fR .HP \w'\fBajtest\fR\ 'u \fBajtest\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBajtest\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Test" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-bsequence\fR \fIseqset\fR .RS 4 .RE .PP \fB\-idresource\fR \fIstring\fR .RS 4 .RE .PP \fB\-taxdir\fR \fIdirectory\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-outseq\fR \fIseqout\fR .RS 4 .RE .PP \fB\-outfeat\fR \fIfeatout\fR .RS 4 .RE .PP \fB\-outdir\fR \fIoutdir\fR .RS 4 Default value: /tmp .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP ajtest is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/matcher.1e0000644000000000000000000001064412214054043012633 0ustar '\" t .\" Title: MATCHER .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "MATCHER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" matcher \- Waterman\-Eggert local alignment of two sequences .SH "SYNOPSIS" .HP \w'\fBmatcher\fR\ 'u \fBmatcher\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR [\fB\-datafile\ \fR\fB\fImatrix\fR\fR] [\fB\-alternatives\ \fR\fB\fIinteger\fR\fR] [\fB\-gapopen\ \fR\fB\fIinteger\fR\fR] [\fB\-gapextend\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIalign\fR\fR .HP \w'\fBmatcher\fR\ 'u \fBmatcher\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBmatcher\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Local" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-asequence\fR \fIsequence\fR .RS 4 .RE .PP \fB\-bsequence\fR \fIsequence\fR .RS 4 .RE .PP \fB\-datafile\fR \fImatrix\fR .RS 4 This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&. .RE .SS "Additional section" .PP \fB\-alternatives\fR \fIinteger\fR .RS 4 This sets the number of alternative matches output\&. By default only the highest scoring alignment is shown\&. A value of 2 gives you other reasonable alignments\&. In some cases, for example multidomain proteins of cDNA and genomic DNA comparisons, there may be other interesting and significant alignments\&. Default value: 1 .RE .PP \fB\-gapopen\fR \fIinteger\fR .RS 4 The gap penalty is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value of 14 assumes you are using the EBLOSUM62 matrix for protein sequences, or a value of 16 and the EDNAFULL matrix for nucleotide sequences\&. Default value: @($(acdprotein)? 14 : 16) .RE .PP \fB\-gapextend\fR \fIinteger\fR .RS 4 The gap length, or gap extension, penalty is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps\&. You can get this result by setting the gap penalty to zero (or very low) and using the gap extension penalty to control gap scoring\&. Default value: @($(acdprotein)? 4 : 4) .RE .SS "Output section" .PP \fB\-outfile\fR \fIalign\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP matcher is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/featcopy.1e0000644000000000000000000000474012214054043013022 0ustar '\" t .\" Title: FEATCOPY .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "FEATCOPY" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" featcopy \- Reads and writes a feature table .SH "SYNOPSIS" .HP \w'\fBfeatcopy\fR\ 'u \fBfeatcopy\fR \fB\-features\ \fR\fB\fIfeatures\fR\fR \fB\-outfeat\ \fR\fB\fIfeatout\fR\fR .HP \w'\fBfeatcopy\fR\ 'u \fBfeatcopy\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBfeatcopy\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Data retrieval:Feature data,Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-features\fR \fIfeatures\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfeat\fR \fIfeatout\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP featcopy is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/einverted.1e0000644000000000000000000000640012214054043013170 0ustar '\" t .\" Title: EINVERTED .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "EINVERTED" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" einverted \- Finds inverted repeats in nucleotide sequences .SH "SYNOPSIS" .HP \w'\fBeinverted\fR\ 'u \fBeinverted\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-gap\ \fR\fB\fIinteger\fR\fR \fB\-threshold\ \fR\fB\fIinteger\fR\fR \fB\-match\ \fR\fB\fIinteger\fR\fR \fB\-mismatch\ \fR\fB\fIinteger\fR\fR [\fB\-maxrepeat\ \fR\fB\fIinteger\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR .HP \w'\fBeinverted\fR\ 'u \fBeinverted\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBeinverted\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Repeats,Nucleic:2D structure" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Required section" .PP \fB\-gap\fR \fIinteger\fR .RS 4 Default value: 12 .RE .PP \fB\-threshold\fR \fIinteger\fR .RS 4 Default value: 50 .RE .PP \fB\-match\fR \fIinteger\fR .RS 4 Default value: 3 .RE .PP \fB\-mismatch\fR \fIinteger\fR .RS 4 Default value: \-4 .RE .SS "Additional section" .PP \fB\-maxrepeat\fR \fIinteger\fR .RS 4 Maximum separation between the start of repeat and the end of the inverted repeat\&. Default value: 2000 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .PP \fB\-outseq\fR \fIseqout\fR .RS 4 The sequence of the inverted repeat regions without gap characters\&. .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP einverted is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/iep.1e0000644000000000000000000000645212214054043011767 0ustar '\" t .\" Title: IEP .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "IEP" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" iep \- Calculate the isoelectric point of proteins .SH "SYNOPSIS" .HP \w'\fBiep\fR\ 'u \fBiep\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-amino\ \fR\fB\fIinteger\fR\fR] [\fB\-carboxyl\ \fR\fB\fIinteger\fR\fR] [\fB\-termini\ \fR\fB\fIboolean\fR\fR] [\fB\-lysinemodified\ \fR\fB\fIinteger\fR\fR] [\fB\-disulphides\ \fR\fB\fIinteger\fR\fR] \fB\-step\ \fR\fB\fIfloat\fR\fR \fB\-plot\ \fR\fB\fItoggle\fR\fR \fB\-report\ \fR\fB\fItoggle\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBiep\fR\ 'u \fBiep\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBiep\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Properties,Display" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Additional section" .PP \fB\-amino\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-carboxyl\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-termini\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-lysinemodified\fR \fIinteger\fR .RS 4 .RE .PP \fB\-disulphides\fR \fIinteger\fR .RS 4 .RE .SS "Advanced section" .PP \fB\-step\fR \fIfloat\fR .RS 4 Default value: \&.5 .RE .SS "Output section" .PP \fB\-plot\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-report\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-graph\fR \fIxygraph\fR .RS 4 .RE .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP iep is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/restrict.1e0000644000000000000000000001717112214054043013051 0ustar '\" t .\" Title: RESTRICT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "RESTRICT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" restrict \- Report restriction enzyme cleavage sites in a nucleotide sequence .SH "SYNOPSIS" .HP \w'\fBrestrict\fR\ 'u \fBrestrict\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-datafile\ \fR\fB\fIdatafile\fR\fR \fB\-mfile\ \fR\fB\fIdatafile\fR\fR \fB\-sitelen\ \fR\fB\fIinteger\fR\fR \fB\-enzymes\ \fR\fB\fIstring\fR\fR \fB\-min\ \fR\fB\fIinteger\fR\fR \fB\-max\ \fR\fB\fIinteger\fR\fR \fB\-solofragment\ \fR\fB\fIboolean\fR\fR \fB\-single\ \fR\fB\fIboolean\fR\fR \fB\-blunt\ \fR\fB\fIboolean\fR\fR \fB\-sticky\ \fR\fB\fIboolean\fR\fR \fB\-ambiguity\ \fR\fB\fIboolean\fR\fR \fB\-plasmid\ \fR\fB\fIboolean\fR\fR \fB\-methylation\ \fR\fB\fIboolean\fR\fR \fB\-commercial\ \fR\fB\fIboolean\fR\fR \fB\-limit\ \fR\fB\fIboolean\fR\fR \fB\-alphabetic\ \fR\fB\fIboolean\fR\fR \fB\-fragments\ \fR\fB\fIboolean\fR\fR \fB\-name\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR .HP \w'\fBrestrict\fR\ 'u \fBrestrict\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBrestrict\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Restriction" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-datafile\fR \fIdatafile\fR .RS 4 .RE .PP \fB\-mfile\fR \fIdatafile\fR .RS 4 Default value: Emethylsites\&.dat .RE .SS "Required section" .PP \fB\-sitelen\fR \fIinteger\fR .RS 4 This sets the minimum length of the restriction enzyme recognition site\&. Any enzymes with sites shorter than this will be ignored\&. Default value: 4 .RE .PP \fB\-enzymes\fR \fIstring\fR .RS 4 The name \*(Aqall\*(Aq reads in all enzyme names from the REBASE database\&. You can specify enzymes by giving their names with commas between then, such as: \*(AqHincII,hinfI,ppiI,hindiii\*(Aq\&. The case of the names is not important\&. You can specify a file of enzyme names to read in by giving the name of the file holding the enzyme names with a \*(Aq@\*(Aq character in front of it, for example, \*(Aq@enz\&.list\*(Aq\&. Blank lines and lines starting with a hash character or \*(Aq!\*(Aq are ignored and all other lines are concatenated together with a comma character \*(Aq,\*(Aq and then treated as the list of enzymes to search for\&. An example of a file of enzyme names is: ! my enzymes HincII, ppiII ! other enzymes hindiii HinfI PpiI Default value: all .RE .SS "Advanced section" .PP \fB\-min\fR \fIinteger\fR .RS 4 This sets the minimum number of cuts for any restriction enzyme that will be considered\&. Any enzymes that cut fewer times than this will be ignored\&. Default value: 1 .RE .PP \fB\-max\fR \fIinteger\fR .RS 4 This sets the maximum number of cuts for any restriction enzyme that will be considered\&. Any enzymes that cut more times than this will be ignored\&. Default value: 2000000000 .RE .PP \fB\-solofragment\fR \fIboolean\fR .RS 4 This gives the fragment lengths of the forward sense strand produced by complete restriction by each restriction enzyme on its own\&. Results are added to the tail section of the report\&. Default value: N .RE .PP \fB\-single\fR \fIboolean\fR .RS 4 If this is set then this forces the values of the mincuts and maxcuts qualifiers to both be 1\&. Any other value you may have set them to will be ignored\&. Default value: N .RE .PP \fB\-blunt\fR \fIboolean\fR .RS 4 This allows those enzymes which cut at the same position on the forward and reverse strands to be considered\&. Default value: Y .RE .PP \fB\-sticky\fR \fIboolean\fR .RS 4 This allows those enzymes which cut at different positions on the forward and reverse strands, leaving an overhang, to be considered\&. Default value: Y .RE .PP \fB\-ambiguity\fR \fIboolean\fR .RS 4 This allows those enzymes which have one or more \*(AqN\*(Aq ambiguity codes in their pattern to be considered Default value: Y .RE .PP \fB\-plasmid\fR \fIboolean\fR .RS 4 If this is set then this allows searches for restriction enzyme recognition site and cut positions that span the end of the sequence to be considered\&. Default value: N .RE .PP \fB\-methylation\fR \fIboolean\fR .RS 4 If this is set then RE recognition sites will not match methylated bases\&. Default value: N .RE .PP \fB\-commercial\fR \fIboolean\fR .RS 4 If this is set, then only those enzymes with a commercial supplier will be searched for\&. This qualifier is ignored if you have specified an explicit list of enzymes to search for, rather than searching through \*(Aqall\*(Aq the enzymes in the REBASE database\&. It is assumed that, if you are asking for an explicit enzyme, then you probably know where to get it from and so all enzymes names that you have asked to be searched for, and which cut, will be reported whether or not they have a commercial supplier\&. Default value: Y .RE .SS "Output section" .PP \fB\-limit\fR \fIboolean\fR .RS 4 This limits the reporting of enzymes to just one enzyme from each group of isoschizomers\&. The enzyme chosen to represent an isoschizomer group is the prototype indicated in the data file \*(Aqembossre\&.equ\*(Aq, which is created by the program \*(Aqrebaseextract\*(Aq\&. If you prefer different prototypes to be used, make a copy of embossre\&.equ in your home directory and edit it\&. If this value is set to be false then all of the input enzymes will be reported\&. You might like to set this to false if you are supplying an explicit set of enzymes rather than searching \*(Aqall\*(Aq of them\&. Default value: Y .RE .PP \fB\-alphabetic\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-fragments\fR \fIboolean\fR .RS 4 This gives the fragment lengths of the forward sense strand produced by complete restriction using all of the input enzymes together\&. Results are added to the tail section of the report\&. Default value: N .RE .PP \fB\-name\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-outfile\fR \fIreport\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP restrict is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/preg.1e0000644000000000000000000000500312214054043012136 0ustar '\" t .\" Title: PREG .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PREG" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" preg \- Regular expression search of protein sequence(s) .SH "SYNOPSIS" .HP \w'\fBpreg\fR\ 'u \fBpreg\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-pattern\ \fR\fB\fIregexp\fR\fR \fB\-outfile\ \fR\fB\fIreport\fR\fR .HP \w'\fBpreg\fR\ 'u \fBpreg\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBpreg\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:Motifs" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-pattern\fR \fIregexp\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIreport\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP preg is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/merger.1e0000644000000000000000000000633712214054043012475 0ustar '\" t .\" Title: MERGER .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "MERGER" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" merger \- Merge two overlapping sequences .SH "SYNOPSIS" .HP \w'\fBmerger\fR\ 'u \fBmerger\fR \fB\-asequence\ \fR\fB\fIsequence\fR\fR \fB\-bsequence\ \fR\fB\fIsequence\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] [\fB\-gapopen\ \fR\fB\fIfloat\fR\fR] [\fB\-gapextend\ \fR\fB\fIfloat\fR\fR] \fB\-outfile\ \fR\fB\fIalign\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR .HP \w'\fBmerger\fR\ 'u \fBmerger\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBmerger\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Consensus" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-asequence\fR \fIsequence\fR .RS 4 .RE .PP \fB\-bsequence\fR \fIsequence\fR .RS 4 .RE .PP \fB\-datafile\fR \fImatrixf\fR .RS 4 This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&. .RE .SS "Additional section" .PP \fB\-gapopen\fR \fIfloat\fR .RS 4 Default value: @($(acdprotein)? 50\&.0 : 50\&.0 ) .RE .PP \fB\-gapextend\fR \fIfloat\fR .RS 4 Default value: @($(acdprotein)? 5\&.0 : 5\&.0) .RE .SS "Output section" .PP \fB\-outfile\fR \fIalign\fR .RS 4 .RE .PP \fB\-outseq\fR \fIseqout\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP merger is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/cirdna.1e0000644000000000000000000001220012214054043012436 0ustar '\" t .\" Title: CIRDNA .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "CIRDNA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" cirdna \- Draws circular maps of DNA constructs .SH "SYNOPSIS" .HP \w'\fBcirdna\fR\ 'u \fBcirdna\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR [\fB\-maxgroups\ \fR\fB\fIinteger\fR\fR] [\fB\-maxlabels\ \fR\fB\fIinteger\fR\fR] \fB\-ruler\ \fR\fB\fIboolean\fR\fR \fB\-blocktype\ \fR\fB\fIlist\fR\fR [\fB\-originangle\ \fR\fB\fIfloat\fR\fR] \fB\-posticks\ \fR\fB\fIselection\fR\fR \fB\-posblocks\ \fR\fB\fIselection\fR\fR [\fB\-intersymbol\ \fR\fB\fIboolean\fR\fR] [\fB\-intercolour\ \fR\fB\fIinteger\fR\fR] [\fB\-interticks\ \fR\fB\fIboolean\fR\fR] [\fB\-gapsize\ \fR\fB\fIinteger\fR\fR] [\fB\-ticklines\ \fR\fB\fIboolean\fR\fR] [\fB\-textheight\ \fR\fB\fIfloat\fR\fR] [\fB\-textlength\ \fR\fB\fIfloat\fR\fR] [\fB\-tickheight\ \fR\fB\fIfloat\fR\fR] [\fB\-blockheight\ \fR\fB\fIfloat\fR\fR] [\fB\-rangeheight\ \fR\fB\fIfloat\fR\fR] [\fB\-gapgroup\ \fR\fB\fIfloat\fR\fR] [\fB\-postext\ \fR\fB\fIfloat\fR\fR] \fB\-graphout\ \fR\fB\fIgraph\fR\fR .HP \w'\fBcirdna\fR\ 'u \fBcirdna\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBcirdna\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Display" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIinfile\fR .RS 4 Default value: inputfile .RE .SS "Additional section" .PP \fB\-maxgroups\fR \fIinteger\fR .RS 4 Default value: 20 .RE .PP \fB\-maxlabels\fR \fIinteger\fR .RS 4 Default value: 10000 .RE .SS "Output section" .PP \fB\-ruler\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-blocktype\fR \fIlist\fR .RS 4 Default value: Filled .RE .PP \fB\-originangle\fR \fIfloat\fR .RS 4 Default value: 90 .RE .PP \fB\-posticks\fR \fIselection\fR .RS 4 Default value: Out .RE .PP \fB\-posblocks\fR \fIselection\fR .RS 4 Default value: In .RE .PP \fB\-intersymbol\fR \fIboolean\fR .RS 4 Default value: Y .RE .PP \fB\-intercolour\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-interticks\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-gapsize\fR \fIinteger\fR .RS 4 Default value: 500 .RE .PP \fB\-ticklines\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-textheight\fR \fIfloat\fR .RS 4 Height of text\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1\&.0 .RE .PP \fB\-textlength\fR \fIfloat\fR .RS 4 Length of text\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1\&.0 .RE .PP \fB\-tickheight\fR \fIfloat\fR .RS 4 Height of ticks\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1\&.0 .RE .PP \fB\-blockheight\fR \fIfloat\fR .RS 4 Height of blocks\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1\&.0 .RE .PP \fB\-rangeheight\fR \fIfloat\fR .RS 4 Height of range ends\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1\&.0 .RE .PP \fB\-gapgroup\fR \fIfloat\fR .RS 4 Space between groups\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1\&.0 .RE .PP \fB\-postext\fR \fIfloat\fR .RS 4 Space between text and ticks, blocks, and ranges\&. Enter a number <1\&.0 or >1\&.0 to decrease or increase the size, respectively Default value: 1\&.0 .RE .PP \fB\-graphout\fR \fIgraph\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP cirdna is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/makenucseq.1e0000644000000000000000000000623112214054043013341 0ustar '\" t .\" Title: MAKENUCSEQ .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "MAKENUCSEQ" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" makenucseq \- Create random nucleotide sequences .SH "SYNOPSIS" .HP \w'\fBmakenucseq\fR\ 'u \fBmakenucseq\fR \fB\-codonfile\ \fR\fB\fIcodon\fR\fR \fB\-amount\ \fR\fB\fIinteger\fR\fR \fB\-length\ \fR\fB\fIinteger\fR\fR [\fB\-useinsert\ \fR\fB\fItoggle\fR\fR] \fB\-insert\ \fR\fB\fIstring\fR\fR \fB\-start\ \fR\fB\fIinteger\fR\fR \fB\-makeseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBmakenucseq\fR\ 'u \fBmakenucseq\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBmakenucseq\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-codonfile\fR \fIcodon\fR .RS 4 Optional codon usage file\&. Nucleotide sequences will be created as triplets matching the frequencies in the file, with the end trimmed to be in the correct reading frame\&. .RE .SS "Required section" .PP \fB\-amount\fR \fIinteger\fR .RS 4 Default value: 100 .RE .PP \fB\-length\fR \fIinteger\fR .RS 4 Default value: 100 .RE .PP \fB\-useinsert\fR \fItoggle\fR .RS 4 Default value: N .RE .PP \fB\-insert\fR \fIstring\fR .RS 4 String that is inserted into sequence .RE .PP \fB\-start\fR \fIinteger\fR .RS 4 Default value: 1 .RE .SS "Output section" .PP \fB\-makeseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP makenucseq is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/syco.1e0000644000000000000000000000604712214054043012167 0ustar '\" t .\" Title: SYCO .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SYCO" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" syco \- Draw synonymous codon usage statistic plot for a nucleotide sequence .SH "SYNOPSIS" .HP \w'\fBsyco\fR\ 'u \fBsyco\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-cfile\ \fR\fB\fIcodon\fR\fR \fB\-window\ \fR\fB\fIinteger\fR\fR \fB\-uncommon\ \fR\fB\fIboolean\fR\fR \fB\-minimum\ \fR\fB\fIfloat\fR\fR \fB\-plot\ \fR\fB\fItoggle\fR\fR \fB\-graph\ \fR\fB\fIxygraph\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBsyco\fR\ 'u \fBsyco\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBsyco\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Codon usage,Nucleic:Gene finding" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 .RE .PP \fB\-cfile\fR \fIcodon\fR .RS 4 Codon usage file .RE .SS "Advanced section" .PP \fB\-window\fR \fIinteger\fR .RS 4 Default value: 30 .RE .PP \fB\-uncommon\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-minimum\fR \fIfloat\fR .RS 4 Default value: \&.15 .RE .SS "Output section" .PP \fB\-plot\fR \fItoggle\fR .RS 4 Default value: Y .RE .PP \fB\-graph\fR \fIxygraph\fR .RS 4 .RE .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP syco is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/taxgetrank.1e0000644000000000000000000000546512214054043013365 0ustar '\" t .\" Title: TAXGETRANK .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "TAXGETRANK" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" taxgetrank \- Get parents of taxon(s) .SH "SYNOPSIS" .HP \w'\fBtaxgetrank\fR\ 'u \fBtaxgetrank\fR \fB\-taxons\ \fR\fB\fItaxon\fR\fR \fB\-rank\ \fR\fB\fIlist\fR\fR \fB\-hidden\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIouttaxon\fR\fR .HP \w'\fBtaxgetrank\fR\ 'u \fBtaxgetrank\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBtaxgetrank\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:Taxonomy" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-taxons\fR \fItaxon\fR .RS 4 .RE .SS "Required section" .PP \fB\-rank\fR \fIlist\fR .RS 4 Multiple ranks can be specified, or \*(Aq*\*(Aq for all Default value: kingdom,phylum,class,order,family,genus,species .RE .SS "Additional section" .SS "Advanced section" .PP \fB\-hidden\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Output section" .PP \fB\-outfile\fR \fIouttaxon\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP taxgetrank is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/getorf.1e0000644000000000000000000001100312214054043012464 0ustar '\" t .\" Title: GETORF .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "GETORF" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" getorf \- Finds and extracts open reading frames (ORFs) .SH "SYNOPSIS" .HP \w'\fBgetorf\fR\ 'u \fBgetorf\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-table\ \fR\fB\fIlist\fR\fR] [\fB\-minsize\ \fR\fB\fIinteger\fR\fR] [\fB\-maxsize\ \fR\fB\fIinteger\fR\fR] [\fB\-find\ \fR\fB\fIlist\fR\fR] \fB\-methionine\ \fR\fB\fIboolean\fR\fR \fB\-circular\ \fR\fB\fIboolean\fR\fR \fB\-reverse\ \fR\fB\fIboolean\fR\fR \fB\-flanking\ \fR\fB\fIinteger\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBgetorf\fR\ 'u \fBgetorf\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBgetorf\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Gene finding" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Additional section" .PP \fB\-table\fR \fIlist\fR .RS 4 .RE .PP \fB\-minsize\fR \fIinteger\fR .RS 4 Default value: 30 .RE .PP \fB\-maxsize\fR \fIinteger\fR .RS 4 Default value: 1000000 .RE .PP \fB\-find\fR \fIlist\fR .RS 4 This is a small menu of possible output options\&. The first four options are to select either the protein translation or the original nucleic acid sequence of the open reading frame\&. There are two possible definitions of an open reading frame: it can either be a region that is free of STOP codons or a region that begins with a START codon and ends with a STOP codon\&. The last three options are probably only of interest to people who wish to investigate the statistical properties of the regions around potential START or STOP codons\&. The last option assumes that ORF lengths are calculated between two STOP codons\&. .RE .SS "Advanced section" .PP \fB\-methionine\fR \fIboolean\fR .RS 4 START codons at the beginning of protein products will usually code for Methionine, despite what the codon will code for when it is internal to a protein\&. This qualifier sets all such START codons to code for Methionine by default\&. Default value: Y .RE .PP \fB\-circular\fR \fIboolean\fR .RS 4 Default value: N .RE .PP \fB\-reverse\fR \fIboolean\fR .RS 4 Set this to be false if you do not wish to find ORFs in the reverse complement of the sequence\&. Default value: Y .RE .PP \fB\-flanking\fR \fIinteger\fR .RS 4 If you have chosen one of the options of the type of sequence to find that gives the flanking sequence around a STOP or START codon, this allows you to set the number of nucleotides either side of that codon to output\&. If the region of flanking nucleotides crosses the start or end of the sequence, no output is given for this codon\&. Default value: 100 .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP getorf is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/seqinfo.1e0000644000000000000000000000471112214054043012652 0ustar '\" t .\" Title: SEQINFO .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SEQINFO" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" seqinfo \- Returns sequence information .SH "SYNOPSIS" .HP \w'\fBseqinfo\fR\ 'u \fBseqinfo\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBseqinfo\fR\ 'u \fBseqinfo\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBseqinfo\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Test" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Default value: stdout .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP seqinfo is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/nospace.1e0000644000000000000000000000513512214054043012637 0ustar '\" t .\" Title: NOSPACE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "NOSPACE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" nospace \- Remove whitespace from an ASCII text file .SH "SYNOPSIS" .HP \w'\fBnospace\fR\ 'u \fBnospace\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR [\fB\-menu\ \fR\fB\fIlist\fR\fR] \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBnospace\fR\ 'u \fBnospace\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBnospace\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .SS "Required section" .SS "Additional section" .PP \fB\-menu\fR \fIlist\fR .RS 4 Default value: all .RE .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP nospace is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/prophet.1e0000644000000000000000000000543212214054043012670 0ustar '\" t .\" Title: PROPHET .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "PROPHET" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" prophet \- Scan one or more sequences with a Gribskov or Henikoff profile .SH "SYNOPSIS" .HP \w'\fBprophet\fR\ 'u \fBprophet\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-gapopen\ \fR\fB\fIfloat\fR\fR \fB\-gapextend\ \fR\fB\fIfloat\fR\fR \fB\-outfile\ \fR\fB\fIalign\fR\fR .HP \w'\fBprophet\fR\ 'u \fBprophet\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBprophet\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Profiles,Protein:Profiles" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .SS "Required section" .PP \fB\-gapopen\fR \fIfloat\fR .RS 4 Default value: 1\&.0 .RE .PP \fB\-gapextend\fR \fIfloat\fR .RS 4 Default value: 1\&.0 .RE .SS "Output section" .PP \fB\-outfile\fR \fIalign\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP prophet is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/acdrelations.1e0000644000000000000000000000570012214054043013655 0ustar '\" t .\" Title: ACDRELATIONS .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ACDRELATIONS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" acdrelations \- Add relations: attribute to ACD files .SH "SYNOPSIS" .HP \w'\fBacdrelations\fR\ 'u \fBacdrelations\fR \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-indir\ \fR\fB\fIdirlist\fR\fR \fB\-inedamfile\ \fR\fB\fIdatafile\fR\fR \fB\-intypefile\ \fR\fB\fIinfile\fR\fR \fB\-outdir\ \fR\fB\fIoutdir\fR\fR .HP \w'\fBacdrelations\fR\ 'u \fBacdrelations\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBacdrelations\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Acd,Data retrieval:Tool data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-mode\fR \fIlist\fR .RS 4 Default value: 1 .RE .PP \fB\-indir\fR \fIdirlist\fR .RS 4 Default value: acdin .RE .PP \fB\-inedamfile\fR \fIdatafile\fR .RS 4 Default value: edamtoacd\&.dat .RE .PP \fB\-intypefile\fR \fIinfile\fR .RS 4 Default value: /homes/jison/emboss/emboss/emboss/acd/knowntypes\&.standard .RE .SS "Required section" .SS "Advanced section" .SS "Output section" .PP \fB\-outdir\fR \fIoutdir\fR .RS 4 Default value: acdout .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP acdrelations is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/origunion.1e0000644000000000000000000000472512214054043013224 0ustar '\" t .\" Title: ORIGUNION .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ORIGUNION" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" origunion \- Reads sequence fragments and builds one sequence .SH "SYNOPSIS" .HP \w'\fBorigunion\fR\ 'u \fBorigunion\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-outseq\ \fR\fB\fIseqout\fR\fR .HP \w'\fBorigunion\fR\ 'u \fBorigunion\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBorigunion\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqout\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP origunion is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/ontogetdown.1e0000644000000000000000000000537012214054043013557 0ustar '\" t .\" Title: ONTOGETDOWN .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "ONTOGETDOWN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" ontogetdown \- Get ontology term(s) by parent id .SH "SYNOPSIS" .HP \w'\fBontogetdown\fR\ 'u \fBontogetdown\fR \fB\-oboterms\ \fR\fB\fIobo\fR\fR [\fB\-obsolete\ \fR\fB\fIboolean\fR\fR] \fB\-outfile\ \fR\fB\fIoutobo\fR\fR .HP \w'\fBontogetdown\fR\ 'u \fBontogetdown\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBontogetdown\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology,Data retrieval:Ontology data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-oboterms\fR \fIobo\fR .RS 4 .RE .SS "Additional section" .PP \fB\-obsolete\fR \fIboolean\fR .RS 4 The default behaviour is to not use or return obsolete terms\&. This option if set will include all terms\&. Default value: N .RE .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutobo\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP ontogetdown is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/chips.1e0000644000000000000000000000504412214054043012314 0ustar '\" t .\" Title: CHIPS .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "CHIPS" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" chips \- Calculates Nc codon usage statistic .SH "SYNOPSIS" .HP \w'\fBchips\fR\ 'u \fBchips\fR \fB\-seqall\ \fR\fB\fIseqall\fR\fR \fB\-sum\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBchips\fR\ 'u \fBchips\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBchips\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Codon usage" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-seqall\fR \fIseqall\fR .RS 4 .RE .SS "Advanced section" .PP \fB\-sum\fR \fIboolean\fR .RS 4 Default value: Y .RE .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP chips is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/tranalign.1e0000644000000000000000000000526512214054043013172 0ustar '\" t .\" Title: TRANALIGN .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "TRANALIGN" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" tranalign \- Generate an alignment of nucleic coding regions from aligned proteins .SH "SYNOPSIS" .HP \w'\fBtranalign\fR\ 'u \fBtranalign\fR \fB\-asequence\ \fR\fB\fIseqall\fR\fR \fB\-bsequence\ \fR\fB\fIseqset\fR\fR [\fB\-table\ \fR\fB\fIlist\fR\fR] \fB\-outseq\ \fR\fB\fIseqoutset\fR\fR .HP \w'\fBtranalign\fR\ 'u \fBtranalign\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBtranalign\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Alignment:Multiple" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-asequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-bsequence\fR \fIseqset\fR .RS 4 .RE .SS "Additional section" .PP \fB\-table\fR \fIlist\fR .RS 4 .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqoutset\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP tranalign is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/msbar.1e0000644000000000000000000001003412214054043012305 0ustar '\" t .\" Title: MSBAR .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "MSBAR" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" msbar \- Mutate a sequence .SH "SYNOPSIS" .HP \w'\fBmsbar\fR\ 'u \fBmsbar\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR \fB\-othersequence\ \fR\fB\fIseqall\fR\fR \fB\-count\ \fR\fB\fIinteger\fR\fR \fB\-point\ \fR\fB\fIlist\fR\fR \fB\-block\ \fR\fB\fIlist\fR\fR \fB\-codon\ \fR\fB\fIlist\fR\fR \fB\-inframe\ \fR\fB\fIboolean\fR\fR \fB\-minimum\ \fR\fB\fIinteger\fR\fR \fB\-maximum\ \fR\fB\fIinteger\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBmsbar\fR\ 'u \fBmsbar\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBmsbar\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Mutation,Protein:Mutation" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIseqall\fR .RS 4 .RE .PP \fB\-othersequence\fR \fIseqall\fR .RS 4 If you require that the resulting mutated sequence should not match a set of other sequences, then you can specify that set of sequences here\&. For example, if you require that the mutated sequence should not be the same as the input sequence, enter the input sequence here\&. If you want the result to be different to previous results of this program, specify the previous result sequences here\&. The program will check that the result does not match the sequences specified here before writing it out\&. If a match is found, then the mutation is started again with a fresh copy of the input sequence\&. If, after 10 such retries, there is still a match to the set of sequence given here, then the matching mutated sequence is written with a warning message\&. Default value: asis:N .RE .SS "Required section" .PP \fB\-count\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-point\fR \fIlist\fR .RS 4 .RE .PP \fB\-block\fR \fIlist\fR .RS 4 .RE .PP \fB\-codon\fR \fIlist\fR .RS 4 Types of codon mutations to perform\&. These are only done if the sequence is nucleic\&. .RE .SS "Additional section" .PP \fB\-inframe\fR \fIboolean\fR .RS 4 Default value: N .RE .SS "Advanced section" .PP \fB\-minimum\fR \fIinteger\fR .RS 4 Default value: 1 .RE .PP \fB\-maximum\fR \fIinteger\fR .RS 4 Default value: 10 .RE .SS "Output section" .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP msbar is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/seqxrefall.1e0000644000000000000000000000576312214054043013364 0ustar '\" t .\" Title: SEQXREFALL .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SEQXREFALL" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" seqxrefall \- Retrieve all cross\-references for a sequence record .SH "SYNOPSIS" .HP \w'\fBseqxrefall\fR\ 'u \fBseqxrefall\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-dbref\ \fR\fB\fIdatafile\fR\fR \fB\-format\ \fR\fB\fIselection\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBseqxrefall\fR\ 'u \fBseqxrefall\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBseqxrefall\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Information" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-sequence\fR \fIsequence\fR .RS 4 The sequence for which cross\-references will be retrieved\&. .RE .PP \fB\-dbref\fR \fIdatafile\fR .RS 4 File of database information including identifier, description, type, URL etc\&. Default value: dbref\&.dat .RE .SS "Required section" .PP \fB\-format\fR \fIselection\fR .RS 4 This specifies the format of the output file Default value: 1 .RE .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 Output file containing list of cross\-references .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP seqxrefall is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/skipredundant.1e0000644000000000000000000001436712214054043014071 0ustar '\" t .\" Title: SKIPREDUNDANT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "SKIPREDUNDANT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" skipredundant \- Remove redundant sequences from an input set .SH "SYNOPSIS" .HP \w'\fBskipredundant\fR\ 'u \fBskipredundant\fR \fB\-feature\ \fR\fB\fItoggle\fR\fR \fB\-sequences\ \fR\fB\fIseqset\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-threshold\ \fR\fB\fIfloat\fR\fR \fB\-minthreshold\ \fR\fB\fIfloat\fR\fR \fB\-maxthreshold\ \fR\fB\fIfloat\fR\fR \fB\-gapopen\ \fR\fB\fIfloat\fR\fR \fB\-gapextend\ \fR\fB\fIfloat\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR \fB\-redundantoutseq\ \fR\fB\fIseqoutall\fR\fR .HP \w'\fBskipredundant\fR\ 'u \fBskipredundant\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBskipredundant\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-feature\fR \fItoggle\fR .RS 4 Sequence feature information will be retained if this option is set\&. .RE .PP \fB\-sequences\fR \fIseqset\fR .RS 4 .RE .PP \fB\-datafile\fR \fImatrixf\fR .RS 4 This is the scoring matrix file used when comparing sequences\&. By default it is the file \*(AqEBLOSUM62\*(Aq (for proteins) or the file \*(AqEDNAFULL\*(Aq (for nucleic sequences)\&. These files are found in the \*(Aqdata\*(Aq directory of the EMBOSS installation\&. .RE .SS "Required section" .PP \fB\-mode\fR \fIlist\fR .RS 4 This option specifies whether to remove redundancy at a single threshold percentage sequence similarity or remove redundancy outside a range of acceptable threshold percentage similarity\&. All permutations of pair\-wise sequence alignments are calculated for each set of input sequences in turn using the EMBOSS implementation of the Needleman and Wunsch global alignment algorithm\&. Redundant sequences are removed in one of two modes as follows: (i) If a pair of proteins achieve greater than a threshold percentage sequence similarity (specified by the user) the shortest sequence is discarded\&. (ii) If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range (specified by the user) the shortest sequence is discarded\&. Default value: 1 .RE .PP \fB\-threshold\fR \fIfloat\fR .RS 4 This option specifies the percentage sequence identity redundancy threshold\&. The percentage sequence identity redundancy threshold determines the redundancy calculation\&. If a pair of proteins achieve greater than this threshold the shortest sequence is discarded\&. Default value: 95\&.0 .RE .PP \fB\-minthreshold\fR \fIfloat\fR .RS 4 This option specifies the percentage sequence identity redundancy threshold (lower limit)\&. The percentage sequence identity redundancy threshold determines the redundancy calculation\&. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded\&. Default value: 30\&.0 .RE .PP \fB\-maxthreshold\fR \fIfloat\fR .RS 4 This option specifies the percentage sequence identity redundancy threshold (upper limit)\&. The percentage sequence identity redundancy threshold determines the redundancy calculation\&. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded\&. Default value: 90\&.0 .RE .PP \fB\-gapopen\fR \fIfloat\fR .RS 4 The gap open penalty is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: @($(acdprotein)? 10\&.0 : 10\&.0 ) .RE .PP \fB\-gapextend\fR \fIfloat\fR .RS 4 The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps\&. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring\&. Default value: @($(acdprotein)? 0\&.5 : 0\&.5 ) .RE .SS "Advanced section" .SS "Output section" .PP \fB\-outseq\fR \fIseqoutall\fR .RS 4 .RE .PP \fB\-redundantoutseq\fR \fIseqoutall\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP skipredundant is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/drfindformat.1e0000644000000000000000000000614212214054043013665 0ustar '\" t .\" Title: DRFINDFORMAT .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "DRFINDFORMAT" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" drfindformat \- Find public databases by format .SH "SYNOPSIS" .HP \w'\fBdrfindformat\fR\ 'u \fBdrfindformat\fR \fB\-query\ \fR\fB\fIstring\fR\fR \fB\-sensitive\ \fR\fB\fIboolean\fR\fR \fB\-subclasses\ \fR\fB\fIboolean\fR\fR \fB\-drfindformat\ \fR\fB\fIoutresource\fR\fR .HP \w'\fBdrfindformat\fR\ 'u \fBdrfindformat\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBdrfindformat\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Ontology:EDAM,Data retrieval:Resource data" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-query\fR \fIstring\fR .RS 4 .RE .SS "Additional section" .SS "Advanced section" .PP \fB\-sensitive\fR \fIboolean\fR .RS 4 By default, the query keywords are matched against the EDAM term names (and synonyms) only\&. This option also matches the keywords against the EDAM term definitions and will therefore (typically) report more matches\&. Default value: N .RE .PP \fB\-subclasses\fR \fIboolean\fR .RS 4 Extend the query matches to include all terms which are specialisations (EDAM sub\-classes) of the matched type\&. Default value: Y .RE .SS "Output section" .PP \fB\-drfindformat\fR \fIoutresource\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP drfindformat is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/manpages/trimspace.1e0000644000000000000000000000503312214054043013173 0ustar '\" t .\" Title: TRIMSPACE .\" Author: Debian Med Packaging Team .\" Generator: DocBook XSL Stylesheets v1.76.1 .\" Date: 05/11/2012 .\" Manual: EMBOSS Manual for Debian .\" Source: EMBOSS 6.4.0 .\" Language: English .\" .TH "TRIMSPACE" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian" .\" ----------------------------------------------------------------- .\" * Define some portability stuff .\" ----------------------------------------------------------------- .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .\" http://bugs.debian.org/507673 .\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html .\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .ie \n(.g .ds Aq \(aq .el .ds Aq ' .\" ----------------------------------------------------------------- .\" * set default formatting .\" ----------------------------------------------------------------- .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .\" ----------------------------------------------------------------- .\" * MAIN CONTENT STARTS HERE * .\" ----------------------------------------------------------------- .SH "NAME" trimspace \- Remove extra whitespace from an ASCII text file .SH "SYNOPSIS" .HP \w'\fBtrimspace\fR\ 'u \fBtrimspace\fR \fB\-infile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR .HP \w'\fBtrimspace\fR\ 'u \fBtrimspace\fR \fB\-help\fR .SH "DESCRIPTION" .PP \fBtrimspace\fR is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Edit" command group(s)\&. .SH "OPTIONS" .SS "Input section" .PP \fB\-infile\fR \fIinfile\fR .RS 4 .RE .SS "Required section" .SS "Additional section" .SS "Advanced section" .SS "Output section" .PP \fB\-outfile\fR \fIoutfile\fR .RS 4 .RE .SH "BUGS" .PP Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&. .SH "SEE ALSO" .PP trimspace is fully documented via the \fBtfm\fR(1) system\&. .SH "AUTHOR" .PP \fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&> .RS 4 Wrote the script used to autogenerate this manual page\&. .RE .SH "COPYRIGHT" .br .PP This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&. .sp debian/watch0000644000000000000000000000011012214054043010202 0ustar version=3 ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-([\d.]*)\.tar\.gz debian/emboss.docs0000644000000000000000000000007612214054043011326 0ustar AUTHORS FAQ NEWS KNOWN_BUGS PROBLEMS THANKS debian/reference debian/upstream0000644000000000000000000000110512214054043010741 0ustar Contact: EMBOSS core development team Homepage: http://emboss.sourceforge.net Name: EMBOSS Reference: title: > EMBOSS: The European Molecular Biology Open Software Suite journal: Trends in Genetics volume: 16 number: 6 pages: 276 - 277 year: 2000 issn: 0168-9525 url: http://www.sciencedirect.com/science/article/B6TCY-40CRS27-G/2/b4e5945c07c58d5a1257cbd685971317 author: Peter Rice and Ian Longden and Alan Bleasby PMID: 10827456 DOI: 10.1016/S0168-9525(00)02024-2 Watch: ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-([\d.]*)\.tar\.gz debian/copyright0000644000000000000000000010546612214054043011130 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.5.7.tar.gz Files: * Copyright: The EMBOSS developers or their employers. License: emboss EMBOSS License (http://emboss.sourceforge.net/licence/) . The AJAX and NUCLEUS libraries are released under the GNU Lesser General Public Licence. . The EMBOSS Administrator’s Guide can be copied, distributed and/or modified under the terms of the GNU Free Documentation License, Version 1.1 or any later version published by the Free Software Foundation; with no Invariant Sections, with no Front-Cover Texts, and with no Back-Cover Texts. A copy of the license is included in the chapter entitled ”GNU Free Documentation License”. . The EMBOSS Quick Guide has been relicenced and can be used, modified and distributed under the same terms as EMBOSS itself. . EMBOSS applications are released under the GNU General Public Licence. . Parsing of ACD files does not constitute a "derived work" and developers are encouraged to do this, for example to write their own GUIs. . For developers who have their own licensing conditions already in effect, there will be an additional way to contribute. The EMBASSY collection can include packages that use the EMBOSS core libraries and interfaces but under their own licensing conditions. They will be bound by the Library GPL of the AJAX and NUCLEUS libraries, but not necessarily by the full GPL. . Some of the suggestions and code examples from David Hanson's book "C Interfaces and Implementations" are included in the AJAX library. This library is available from http://www.cs.princeton.edu/software/cii/ or ftp://ftp.cs.princeton.edu/pub/packages/cii/ . The COPYRIGHT file in release 1.10 says: . > The author of this software is David R. Hanson. > > Copyright (c) 1994,1995,1996 by David R. Hanson. All Rights Reserved. > > Permission to use, copy, modify, and distribute this software for any > purpose, subject to the provisions described below, without fee is > hereby granted, provided that this entire notice is included in all > copies of any software that is or includes a copy or modification of > this software and in all copies of the supporting documentation for > such software. > > THIS SOFTWARE IS BEING PROVIDED "AS IS", WITHOUT ANY EXPRESS OR IMPLIED > WARRANTY. IN PARTICULAR, THE AUTHOR DOES MAKE ANY REPRESENTATION OR > WARRANTY OF ANY KIND CONCERNING THE MERCHANTABILITY OF THIS SOFTWARE OR > ITS FITNESS FOR ANY PARTICULAR PURPOSE. > > David Hanson / drh@cs.princeton.edu / http://www.cs.princeton.edu/~drh/ > Wed Apr 24 13:44:16 PDT 1996 > Mon Dec 12 15:58:13 EST 1994 Comment: On Debian systems, the complete text of the GNU General Public License version 2, the GNU Free Documentation License version 1.2, and the GNU Library Public License version 2 can be found in ‘/usr/share/common-licenses/GPL-2’, ‘/usr/share/common-licenses/GFDL-1.2’ and ‘/usr/share/common-licenses/LGPL-2’ respectively. Files: ajax/pcre/* Copyright: © 1997-2000 University of Cambridge License: PCRE PCRE is a library of functions to support regular expressions whose syntax and semantics are as close as possible to those of the Perl 5 language. . Written by: Philip Hazel . University of Cambridge Computing Service, Cambridge, England. Phone: +44 1223 334714. . Copyright (c) 1997-2000 University of Cambridge . Permission is granted to anyone to use this software for any purpose on any computer system, and to redistribute it freely, subject to the following restrictions: . 1. This software is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. . 2. The origin of this software must not be misrepresented, either by explicit claim or by omission. In practice, this means that if you use PCRE in software which you distribute to others, commercially or otherwise, you must put a sentence like this . Regular expression support is provided by the PCRE library package, which is open source software, written by Philip Hazel, and copyright by the University of Cambridge, England. . somewhere reasonably visible in your documentation and in any relevant files or online help data or similar. A reference to the ftp site for the source, that is, to . ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/ . should also be given in the documentation. . 3. Altered versions must be plainly marked as such, and must not be misrepresented as being the original software. . 4. If PCRE is embedded in any software that is released under the GNU General Purpose Licence (GPL), then the terms of that licence shall supersede any condition above with which it is incompatible. Files: plplot/* Copyright: © 1987, 1988 by Digital Equipment Corporation, Maynard, Massachusetts, © 1991, 1993, 1994 Wesley Ebisuzaki © 1992, 1993, 1994, 1995, 2001, 2002, 2004 Maurice LeBrun © 1992, 1999, 2001 Geoffrey Furnish © 1992, Maurice J. LeBrun, Geoff Furnish, Tony Richardson. © 2000, 2001, 2002, 2004, 2005 Alan W. Irwin © 2000, 2001, 2002, 2003, 2004 Joao Cardoso © 2001, 2003, 2004, 2005 Rafael Laboissiere © 2001, 2002, 2003, 2004 Andrew Roach © 2002, Vincent Darley © 2004, 2005 Thomas J. Duck © 2004, 2005, 2006 Andrew Ross © 2006, Hazen Babcock © 2006, Jim Dishaw © 2006, Werner Smekal License: GPL-2+ This library is free software; you can redistribute it and/or modify it under the terms of the GNU Library General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Library General Public License for more details. . You should have received a copy of the GNU Library General Public License along with this library; if not, write to the Free Software Foundation, Inc. 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA Files: ajax/zlib/* Copyright: © 1995-2005 Jean-loup Gailly and Mark Adler License: zlib This software is provided 'as-is', without any express or implied warranty. In no event will the authors be held liable for any damages arising from the use of this software. . Permission is granted to anyone to use this software for any purpose, including commercial applications, and to alter it and redistribute it freely, subject to the following restrictions: . 1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required. 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. 3. This notice may not be removed or altered from any source distribution. . Jean-loup Gailly Mark Adler jloup@gzip.org madler@alumni.caltech.edu Files: doc/programs/html/antigenic.html doc/programs/html/pasteseq.html doc/programs/html/showpep.html doc/programs/master/emboss/apps/inc/acdc.input doc/programs/master/emboss/apps/inc/acdlog.input doc/programs/master/emboss/apps/inc/acdtrace.input doc/programs/master/emboss/apps/inc/antigenic.input doc/programs/master/emboss/apps/inc/pasteseq.input doc/programs/master/emboss/apps/inc/showpep.input doc/programs/text/antigenic.txt doc/programs/text/pasteseq.txt doc/programs/text/showpep.txt emboss/data/dbxref.txt test/data/amir.swiss test/data/uniprotft.sw test/swiss/seq.dat test/swnew/trembl.dat Copyright: none These files are marked to be copyrighted by the UniProt Consortium, but this applies to the UniProt database as a whole, not to the individual records. License: not-the-CC-BY-ND-3.0 Despite the following statement: . Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms Distributed under the Creative Commons Attribution-NoDerivs License . The above files, as individual records, are not copyrighted. The statement is for the UniProt as a whole. Files: ajax/core/ajvarbcf.c Copyright: © 2010 Broad Institute © The EMBOSS developers License: LGPL-2.1+ and MIT /* @source ajvarbcf *********************************************************** ** ** BCF files reading/writing functions ** ** @version $Revision: 1.5 $ ** @modified 2011 Mahmut Uludag ported from bcftools project (samtools.sf.net) ** @modified $Date: 2012/07/14 14:52:39 $ by $Author: rice $ ** @@ ** ** This library is free software; you can redistribute it and/or ** modify it under the terms of the GNU Lesser General Public ** License as published by the Free Software Foundation; either ** version 2.1 of the License, or (at your option) any later version. ** ** This library is distributed in the hope that it will be useful, ** but WITHOUT ANY WARRANTY; without even the implied warranty of ** MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU ** Lesser General Public License for more details. ** ** You should have received a copy of the GNU Lesser General Public ** License along with this library; if not, write to the Free Software ** Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, ** MA 02110-1301, USA. ** ******************************************************************************/ . /* The MIT License . Copyright (c) 2010 Broad Institute . Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: . The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. . THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. */ Files: emboss/data/TAXONOMY/*.dmp Homepage: http://www.ncbi.nlm.nih.gov/taxonomy Copyright: Probably public domain (under investigation). License: CC-BY-3.0 Files: emboss/data/OBO/*.obo Homepage: http://code.google.com/p/obo-relations/ Copyright: 2008-2013 Chris Mungall et all License: CC-BY-3.0 Comment: see http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=694908 Files: emboss/data/OBO/gene_ontology*.obo Homepage: http://www.geneontology.org/GO.cite.shtml Copyright: 1999–2013 Gene Ontology Consortium Comment: License is clarified at https://www.ebi.ac.uk/panda/jira/browse/GOHELP-147 License: CC-BY-3.0 Files: emboss/data/OBO/chebi.obo Homepage: http://www.ebi.ac.uk/chebi/ Copyright: Public domain according to answer or authors available at https://lists.debian.org/debian-med/2013/01/msg00012.html License: CC-BY-3.0 Files: emboss/data/OBO/software.obo Homepage: http://theswo.sourceforge.net/ Copyright: 2011-2012 James Malone Comment: The statement of the author can be seen at http://bugs.debian.org/694908#92 as long as the license is not yet published on its homepage License: Apache-2.0 On Debian systems you can find the complete text of the Apache License Version 2.0 at /usr/share/common-licenses/Apache-2.0. Files: emboss/data/OBO/pathway.obo Homepage: http://www.obofoundry.org/cgi-bin/detail.cgi?id=pathway Source: ftp://rgd.mcw.edu/pub/data_release/ Copyright: 2009-2012 Victoria Petri License: CC-BY-3.0 Comment: See ftp://rgd.mcw.edu/pub/data_release/PathwayOntology_introduction.doc Files: emboss/data/OBO/eco.obo Homepage: https://code.google.com/p/evidenceontology/ Copyright: 2009-2013 Marcus Chibucos , Michelle Giglio License: GPL-3+ Files: emboss/data/OBO/ro.obo Homepage: http://code.google.com/p/obo-relations/ Copyright: 2009-2013 Chris Mungall and others License: CC-BY-3.0 Files: emboss/data/OBO/so.obo Homepage: http://www.sequenceontology.org/ Copyright: 2009-2013 Sequence Ontology Karen Eilbeck License: PD The Sequence Ontology is in the public domain. It is available to public and private sector users with no licensing requirements. We ask that you cite SO and do not make changes to SO then redistribute under the same name. . See http://www.sequenceontology.org/resources/faq.html#lic Files: debian/* Copyright: 2002-2004 Matt Hope 2007-2013 Charles Plessy 2012-2013 Andreas Tille License: LGPL-2.1+ Comment: The EMBOSS package for Debian was initially prepared by Matt Hope (dopey@debian.org) in 2002-2004 and released on (http://debian.bioinformatics.unsw.edu.au/). The package distributed in Debian was prepared by the "pkg-emboss" project in 2006, using the work of Matt Hope as a starting point. Feel free to use the work of the pkg-emboss project as if it were in the public domain. The license of the packaging (LGPL-2.1+) was chosen in 2013 to be as close as possible to upstream's licenses (LGPL-2.1+ for the libraries, GPL-2+ for the applications, and GFDL-NIV-1.1 for some of the documentation). After applyint patches, please be kind to submit them to Upstream under terms that are convenient for them. License: CC-BY-3.0 Attribution 3.0 Unported . CREATIVE COMMONS CORPORATION IS NOT A LAW FIRM AND DOES NOT PROVIDE LEGAL SERVICES. DISTRIBUTION OF THIS LICENSE DOES NOT CREATE AN ATTORNEY-CLIENT RELATIONSHIP. CREATIVE COMMONS PROVIDES THIS INFORMATION ON AN "AS-IS" BASIS. CREATIVE COMMONS MAKES NO WARRANTIES REGARDING THE INFORMATION PROVIDED, AND DISCLAIMS LIABILITY FOR DAMAGES RESULTING FROM ITS USE. . License . THE WORK (AS DEFINED BELOW) IS PROVIDED UNDER THE TERMS OF THIS CREATIVE COMMONS PUBLIC LICENSE ("CCPL" OR "LICENSE"). THE WORK IS PROTECTED BY COPYRIGHT AND/OR OTHER APPLICABLE LAW. ANY USE OF THE WORK OTHER THAN AS AUTHORIZED UNDER THIS LICENSE OR COPYRIGHT LAW IS PROHIBITED. . BY EXERCISING ANY RIGHTS TO THE WORK PROVIDED HERE, YOU ACCEPT AND AGREE TO BE BOUND BY THE TERMS OF THIS LICENSE. TO THE EXTENT THIS LICENSE MAY BE CONSIDERED TO BE A CONTRACT, THE LICENSOR GRANTS YOU THE RIGHTS CONTAINED HERE IN CONSIDERATION OF YOUR ACCEPTANCE OF SUCH TERMS AND CONDITIONS. . 1. Definitions . a. "Adaptation" means a work based upon the Work, or upon the Work and other pre-existing works, such as a translation, adaptation, derivative work, arrangement of music or other alterations of a literary or artistic work, or phonogram or performance and includes cinematographic adaptations or any other form in which the Work may be recast, transformed, or adapted including in any form recognizably derived from the original, except that a work that constitutes a Collection will not be considered an Adaptation for the purpose of this License. For the avoidance of doubt, where the Work is a musical work, performance or phonogram, the synchronization of the Work in timed-relation with a moving image ("synching") will be considered an Adaptation for the purpose of this License. b. "Collection" means a collection of literary or artistic works, such as encyclopedias and anthologies, or performances, phonograms or broadcasts, or other works or subject matter other than works listed in Section 1(f) below, which, by reason of the selection and arrangement of their contents, constitute intellectual creations, in which the Work is included in its entirety in unmodified form along with one or more other contributions, each constituting separate and independent works in themselves, which together are assembled into a collective whole. A work that constitutes a Collection will not be considered an Adaptation (as defined above) for the purposes of this License. c. "Distribute" means to make available to the public the original and copies of the Work or Adaptation, as appropriate, through sale or other transfer of ownership. d. "Licensor" means the individual, individuals, entity or entities that offer (s) the Work under the terms of this License. e. "Original Author" means, in the case of a literary or artistic work, the individual, individuals, entity or entities who created the Work or if no individual or entity can be identified, the publisher; and in addition (i) in the case of a performance the actors, singers, musicians, dancers, and other persons who act, sing, deliver, declaim, play in, interpret or otherwise perform literary or artistic works or expressions of folklore; (ii) in the case of a phonogram the producer being the person or legal entity who first fixes the sounds of a performance or other sounds; and, (iii) in the case of broadcasts, the organization that transmits the broadcast. f. "Work" means the literary and/or artistic work offered under the terms of this License including without limitation any production in the literary, scientific and artistic domain, whatever may be the mode or form of its expression including digital form, such as a book, pamphlet and other writing; a lecture, address, sermon or other work of the same nature; a dramatic or dramatico-musical work; a choreographic work or entertainment in dumb show; a musical composition with or without words; a cinematographic work to which are assimilated works expressed by a process analogous to cinematography; a work of drawing, painting, architecture, sculpture, engraving or lithography; a photographic work to which are assimilated works expressed by a process analogous to photography; a work of applied art; an illustration, map, plan, sketch or three-dimensional work relative to geography, topography, architecture or science; a performance; a broadcast; a phonogram; a compilation of data to the extent it is protected as a copyrightable work; or a work performed by a variety or circus performer to the extent it is not otherwise considered a literary or artistic work. g. "You" means an individual or entity exercising rights under this License who has not previously violated the terms of this License with respect to the Work, or who has received express permission from the Licensor to exercise rights under this License despite a previous violation. h. "Publicly Perform" means to perform public recitations of the Work and to communicate to the public those public recitations, by any means or process, including by wire or wireless means or public digital performances; to make available to the public Works in such a way that members of the public may access these Works from a place and at a place individually chosen by them; to perform the Work to the public by any means or process and the communication to the public of the performances of the Work, including by public digital performance; to broadcast and rebroadcast the Work by any means including signs, sounds or images. i. "Reproduce" means to make copies of the Work by any means including without limitation by sound or visual recordings and the right of fixation and reproducing fixations of the Work, including storage of a protected performance or phonogram in digital form or other electronic medium. . 2. Fair Dealing Rights. Nothing in this License is intended to reduce, limit, or restrict any uses free from copyright or rights arising from limitations or exceptions that are provided for in connection with the copyright protection under copyright law or other applicable laws. . 3. License Grant. Subject to the terms and conditions of this License, Licensor hereby grants You a worldwide, royalty-free, non-exclusive, perpetual (for the duration of the applicable copyright) license to exercise the rights in the Work as stated below: . a. to Reproduce the Work, to incorporate the Work into one or more Collections, and to Reproduce the Work as incorporated in the Collections; b. to create and Reproduce Adaptations provided that any such Adaptation, including any translation in any medium, takes reasonable steps to clearly label, demarcate or otherwise identify that changes were made to the original Work. For example, a translation could be marked "The original work was translated from English to Spanish," or a modification could indicate "The original work has been modified."; c. to Distribute and Publicly Perform the Work including as incorporated in Collections; and, d. to Distribute and Publicly Perform Adaptations. e. For the avoidance of doubt: . i. Non-waivable Compulsory License Schemes. In those jurisdictions in which the right to collect royalties through any statutory or compulsory licensing scheme cannot be waived, the Licensor reserves the exclusive right to collect such royalties for any exercise by You of the rights granted under this License; ii. Waivable Compulsory License Schemes. In those jurisdictions in which the right to collect royalties through any statutory or compulsory licensing scheme can be waived, the Licensor waives the exclusive right to collect such royalties for any exercise by You of the rights granted under this License; and, iii. Voluntary License Schemes. The Licensor waives the right to collect royalties, whether individually or, in the event that the Licensor is a member of a collecting society that administers voluntary licensing schemes, via that society, from any exercise by You of the rights granted under this License. . The above rights may be exercised in all media and formats whether now known or hereafter devised. The above rights include the right to make such modifications as are technically necessary to exercise the rights in other media and formats. Subject to Section 8(f), all rights not expressly granted by Licensor are hereby reserved. . 4. Restrictions. The license granted in Section 3 above is expressly made subject to and limited by the following restrictions: . a. You may Distribute or Publicly Perform the Work only under the terms of this License. You must include a copy of, or the Uniform Resource Identifier (URI) for, this License with every copy of the Work You Distribute or Publicly Perform. You may not offer or impose any terms on the Work that restrict the terms of this License or the ability of the recipient of the Work to exercise the rights granted to that recipient under the terms of the License. You may not sublicense the Work. You must keep intact all notices that refer to this License and to the disclaimer of warranties with every copy of the Work You Distribute or Publicly Perform. When You Distribute or Publicly Perform the Work, You may not impose any effective technological measures on the Work that restrict the ability of a recipient of the Work from You to exercise the rights granted to that recipient under the terms of the License. This Section 4(a) applies to the Work as incorporated in a Collection, but this does not require the Collection apart from the Work itself to be made subject to the terms of this License. If You create a Collection, upon notice from any Licensor You must, to the extent practicable, remove from the Collection any credit as required by Section 4(b), as requested. If You create an Adaptation, upon notice from any Licensor You must, to the extent practicable, remove from the Adaptation any credit as required by Section 4(b), as requested. b. If You Distribute, or Publicly Perform the Work or any Adaptations or Collections, You must, unless a request has been made pursuant to Section 4 (a), keep intact all copyright notices for the Work and provide, reasonable to the medium or means You are utilizing: (i) the name of the Original Author (or pseudonym, if applicable) if supplied, and/or if the Original Author and/or Licensor designate another party or parties (e.g., a sponsor institute, publishing entity, journal) for attribution ("Attribution Parties") in Licensor's copyright notice, terms of service or by other reasonable means, the name of such party or parties; (ii) the title of the Work if supplied; (iii) to the extent reasonably practicable, the URI, if any, that Licensor specifies to be associated with the Work, unless such URI does not refer to the copyright notice or licensing information for the Work; and (iv) , consistent with Section 3(b), in the case of an Adaptation, a credit identifying the use of the Work in the Adaptation (e.g., "French translation of the Work by Original Author," or "Screenplay based on original Work by Original Author"). The credit required by this Section 4 (b) may be implemented in any reasonable manner; provided, however, that in the case of a Adaptation or Collection, at a minimum such credit will appear, if a credit for all contributing authors of the Adaptation or Collection appears, then as part of these credits and in a manner at least as prominent as the credits for the other contributing authors. For the avoidance of doubt, You may only use the credit required by this Section for the purpose of attribution in the manner set out above and, by exercising Your rights under this License, You may not implicitly or explicitly assert or imply any connection with, sponsorship or endorsement by the Original Author, Licensor and/or Attribution Parties, as appropriate, of You or Your use of the Work, without the separate, express prior written permission of the Original Author, Licensor and/or Attribution Parties. c. Except as otherwise agreed in writing by the Licensor or as may be otherwise permitted by applicable law, if You Reproduce, Distribute or Publicly Perform the Work either by itself or as part of any Adaptations or Collections, You must not distort, mutilate, modify or take other derogatory action in relation to the Work which would be prejudicial to the Original Author's honor or reputation. Licensor agrees that in those jurisdictions (e.g. Japan), in which any exercise of the right granted in Section 3(b) of this License (the right to make Adaptations) would be deemed to be a distortion, mutilation, modification or other derogatory action prejudicial to the Original Author's honor and reputation, the Licensor will waive or not assert, as appropriate, this Section, to the fullest extent permitted by the applicable national law, to enable You to reasonably exercise Your right under Section 3(b) of this License (right to make Adaptations) but not otherwise. . 5. Representations, Warranties and Disclaimer . UNLESS OTHERWISE MUTUALLY AGREED TO BY THE PARTIES IN WRITING, LICENSOR OFFERS THE WORK AS-IS AND MAKES NO REPRESENTATIONS OR WARRANTIES OF ANY KIND CONCERNING THE WORK, EXPRESS, IMPLIED, STATUTORY OR OTHERWISE, INCLUDING, WITHOUT LIMITATION, WARRANTIES OF TITLE, MERCHANTIBILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT OR OTHER DEFECTS, ACCURACY, OR THE PRESENCE OF ABSENCE OF ERRORS, WHETHER OR NOT DISCOVERABLE. SOME JURISDICTIONS DO NOT ALLOW THE EXCLUSION OF IMPLIED WARRANTIES, SO SUCH EXCLUSION MAY NOT APPLY TO YOU. . 6. Limitation on Liability. . EXCEPT TO THE EXTENT REQUIRED BY APPLICABLE LAW, IN NO EVENT WILL LICENSOR BE LIABLE TO YOU ON ANY LEGAL THEORY FOR ANY SPECIAL, INCIDENTAL, CONSEQUENTIAL, PUNITIVE OR EXEMPLARY DAMAGES ARISING OUT OF THIS LICENSE OR THE USE OF THE WORK, EVEN IF LICENSOR HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. . 7. Termination . a. This License and the rights granted hereunder will terminate automatically upon any breach by You of the terms of this License. Individuals or entities who have received Adaptations or Collections from You under this License, however, will not have their licenses terminated provided such individuals or entities remain in full compliance with those licenses. Sections 1, 2, 5, 6, 7, and 8 will survive any termination of this License. b. Subject to the above terms and conditions, the license granted here is perpetual (for the duration of the applicable copyright in the Work). Notwithstanding the above, Licensor reserves the right to release the Work under different license terms or to stop distributing the Work at any time; provided, however that any such election will not serve to withdraw this License (or any other license that has been, or is required to be, granted under the terms of this License), and this License will continue in full force and effect unless terminated as stated above. . 8. Miscellaneous . a. Each time You Distribute or Publicly Perform the Work or a Collection, the Licensor offers to the recipient a license to the Work on the same terms and conditions as the license granted to You under this License. b. Each time You Distribute or Publicly Perform an Adaptation, Licensor offers to the recipient a license to the original Work on the same terms and conditions as the license granted to You under this License. c. If any provision of this License is invalid or unenforceable under applicable law, it shall not affect the validity or enforceability of the remainder of the terms of this License, and without further action by the parties to this agreement, such provision shall be reformed to the minimum extent necessary to make such provision valid and enforceable. d. No term or provision of this License shall be deemed waived and no breach consented to unless such waiver or consent shall be in writing and signed by the party to be charged with such waiver or consent. e. This License constitutes the entire agreement between the parties with respect to the Work licensed here. There are no understandings, agreements or representations with respect to the Work not specified here. Licensor shall not be bound by any additional provisions that may appear in any communication from You. This License may not be modified without the mutual written agreement of the Licensor and You. f. The rights granted under, and the subject matter referenced, in this License were drafted utilizing the terminology of the Berne Convention for the Protection of Literary and Artistic Works (as amended on September 28, 1979), the Rome Convention of 1961, the WIPO Copyright Treaty of 1996, the WIPO Performances and Phonograms Treaty of 1996 and the Universal Copyright Convention (as revised on July 24, 1971). These rights and subject matter take effect in the relevant jurisdiction in which the License terms are sought to be enforced according to the corresponding provisions of the implementation of those treaty provisions in the applicable national law. If the standard suite of rights granted under applicable copyright law includes additional rights not granted under this License, such additional rights are deemed to be included in the License; this License is not intended to restrict the license of any rights under applicable law. . Creative Commons Notice . Creative Commons is not a party to this License, and makes no warranty whatsoever in connection with the Work. Creative Commons will not be liable to You or any party on any legal theory for any damages whatsoever, including without limitation any general, special, incidental or consequential damages arising in connection to this license. Notwithstanding the foregoing two (2) sentences, if Creative Commons has expressly identified itself as the Licensor hereunder, it shall have all rights and obligations of Licensor. . Except for the limited purpose of indicating to the public that the Work is licensed under the CCPL, Creative Commons does not authorize the use by either party of the trademark "Creative Commons" or any related trademark or logo of Creative Commons without the prior written consent of Creative Commons. Any permitted use will be in compliance with Creative Commons' then-current trademark usage guidelines, as may be published on its website or otherwise made available upon request from time to time. For the avoidance of doubt, this trademark restriction does not form part of this License. . Creative Commons may be contacted at http://creativecommons.org/. License: GPL-3+ This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. . This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . . On Debian systems, the complete text of the GNU General Public License version 3 can be found at /usr/share/common-licenses/GPL-3. License: LGPL-2.1+ This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2.1 of the License, or (at your option) any later version. . This library is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. . You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA Comment: On Debian systems, the complete text of the GNU Lesser General Public License version 2.1 can be found at /usr/share/common-licenses/LGPL-2.1. debian/source/0000755000000000000000000000000012214054043010461 5ustar debian/source/format0000644000000000000000000000001412214054043011667 0ustar 3.0 (quilt) debian/emboss.dirs0000644000000000000000000000011112214054043011325 0ustar usr/bin #usr/share/applications etc/emboss/embossrc.d usr/share/man/man1 debian/EMBOSS_qg_new.pdf.uu0000644000000000000000000051057412214054043012650 0ustar begin 644 EMBOSS_qg_new.pdf M)5!$1BTQ+C0-)>+CS],-"C(P(#`@;V)J(#P\+TQI;F5A"A[UU>#45,AV0N<&U1>J#=,)OQ/L,/MABHE?P,C*?N`6DF M(+8&8F$&QIM`^Q@8@?@U0(`!`-,V)#(-96YD%LP(#`@-3DU+C(R(#@T,ETO4&%R96YT(#$W(#`@4B]#;VYT96YT'1= M+T5X=$=3=&%T93P\+T=3,2`R-R`P(%(^/CX^#65N9&]B:@TR-"`P(&]B:CP\ M+U-U8G1Y<&4O5')U951Y<&4O1F]N=$1E7!E+T9O;G0^/@UE;F1O M8FH-,C4@,"!O8FH\/"]3=6)T>7!E+U1R=654>7!E+T9O;G1$97-C'1'4W1A=&4O4T$@ M9F%LT",W#<[_K\]U]K@[S MU?7VZO-V:U2NMONK3&T*K^!_IEQ1IK9255ZD7FV?KC[?S%ZU,[S@O[D=KS99 MFF49/+9`MWV]2FZ_7'^]OU=Z^P,9Y75:`UOZ"^R`3VE6=DCK*J0E-J9"#M^2 MWW5>IGFB_C[W>N-2E[2Z2.OD49=IF2B]R0V\WH7'G=[8M$@ZI;]O_T*955J! MRO@G4[:NT^J=P-SE0:#):Q9XJWUJDS-(*9/3]*PWID".&I!#1P=W">M/&`H:Z!I$Q]TJ.2=J44]'`_R/DFY.JK MKD'0,VG4,:^1+DH[F]Q/>PUBJV0!/JE)7H$[HD3I0L+(NLB`,&C::V/@*I01 M47R7I\861FW_P&B&D,9@IB;W_)AF-G.(\2WY$\+BT$"?S-I@*!8TMDZF$U[K MY(VY0X+9F&`7U`7]>Q1SPJ,WP"O"C(A`[^`UI0@$I=<'FOP M8@X"J_4L*S@_!40T.@/$HQ"L?)R%220%GN`S)U,0]1S(V\?PZ_!!J5M=(*,[73B0?*,+&WZK8Y`ZA_"Q M?8'K"4Z0/8DN+W+VFC)@UVG28<=FH4?6E&^47 MV.(P><`VX,!9G%&&AO<,I)%2Z'+!@1),5+@>*1LM&EN1`:3_$]2V`])&YP`\ M/1*2PT(T6.D+YA.4P-`U3+83+GV0?%#M)+`GG>?$$@Z(XJGM&V$SH'>@QF81 M_A,+Q%/Y^Z#02)ZR.:Q?]A2^@>HXX@(^32#-CF<;Q0C\A;YF=J5Y1JI MUY`);?LH/P[$!$*$_4!!Q-$#-]JAU^XT,DPUM)2:?`:=RY7\@%0K&MZH^G<8 MZ\COI=/!!8X#1RH^/^F*RXK-8.C"=JA7UD'TFS7EDFI$PTO7V#K6L?7LFA:3 MK"!)6,[#H*E#-0\"F+0-[=*C"$1>^H`^:NPGBI'VVE$.'2Y))DV-],S'L]"! MDHZ:)?GX5><9=SX4O1Q#:QF)D2!!N5GJ\18+_5H7'HZ1V7:+&"L*"GC'AS#H M^`UIF M*`/JU!9@;&LX@*M.1>@TFXUY*] M>!&NS3!`?[$TW819OS`&]]V>#`+7LD$3&S1@:+!\1SD/EU)/V"LL)AB3,,H\ MTU2!X#\(9(@.^75K@.2U14A>Z0$X=HUP9`UE_O"5&J/A/DFI!)<3+4B4843Z M<";D(KQ3JRJI(/%LL12*1&X[G?$I*]TF6:J>`_]@H.PWQ^8E*">0!\&,GS7$5459O#3US/X@[$%$<+R\G1*BYOWO97'+2D'A.Q'./A5`'9H+;LJ"&CQW.CC)(AZV5%VS2 M4S`5M?0ZX/S$9:_D^14)1[ZU+$*`[^6R9@W.#](4N.*W@3#_G\%9E!?U,4_[ M!;=`VFL\<385SP]#^PT63ZII#?_O&7$QB%WXXMMB@=0)CUQ0QUU^V2"4+,#/ M-)ELY'H;AI<0G(E\D%DH@VK'@UG)#!WE&BKIPY0/WU(\A][+H"6A"],S3-Q; M5AUVQP(V1]@+OO)><(_P`@Z/SE*R'Q#/(L[7'T'5B\F_D!)5$A>%[^I?`08` MS/S,A@UE;F1S=')E86T-96YD;V)J#3(Y(#`@;V)J/#PO3&5N9W1H(#$W,SN2(N4KU:N\(LR MS_I+YD*U\'G+2\RSP=V%2#>=[C\K?79QH5S4^9,+M.O=7;&D=:25%I!F)V%- M^=[14N40C-V9+DE_UQW!_)*USV!H:2U)I\D]VL'&W24V\PA%V2,X(.V$^P<[ MAA>?W%V,.6S.VF&7N;_6%JE8!`[5'7TFC=2QWYS9RD:C4.;GWH6"C.Y(!#FR MU\L3.<^.D,J&O+L3]T1)0S%('+5_7"J)AL+4,+L>#L*WU0W.,FC2N_;X(AZP MS6271R0*WHJ6A0MAIO37T:4ENT;^1R$7(=/V[3AYE>(DZVH(F[S3 M)9LDJ@CC=$N.]M?R.$HM/)N%VI?1LK)H--;$FT0KVS_(^P6\G]=,JBV3)'>8 M&)FTU5O.P<;D8.F^$#=*]'Q^Q/HB')9O'OD6$&5O^1:0;T'SS7.^/6V$)TRR MC`?&("-)YO9O^[IZHU(O9%Q`&HHCXPEZ3C-]+/0BCS+IN/7G!#^@>I[3/EI. M!^\UT@\=QX:B@O7,KR7.0R4'[K4+GB/\R#(;BBW'<8/+GB\;NZE=T3J'2QT$,LUJ9,A0O8$"PP'S9"M^?3)>4Y_ M67S^-("^AV_F(P%@5=/Y0N/[_7H=,@KI'I$6T)9(%[7`]U)C_+9WOA9T#6I= M9(^&BR6P7`X,JD7^,(F.*AJUDYJI'X1*Q:ZY[7D*/+50CD>JB)\SA;LJW[QS ML2"OWKB2P>&]*Q/1K5S)\5YQJZ7P;97MY/CN/,&_B&J=X#NCAR<+;3WV6[UH MQ_Z$LT&-,*R_6(MAJ?W(89]9J"_97Z:7%9YCKV00WNDR0,$%W#M31-WA2;\' MEQI:=E_$X6Q`;UDJL@]BT&3(O`E\71J_N/I:$H,E38O<.B*W/@!]$P"2_-TB M-=_"=O2I;6?)?NFRC[F*4R4?>-*I\K?JPD>'_&R/)O,D>?V9,*M&7HKC\P*C MH.QA8V?%L3V!Q-KL"_:6V3,1DMFO:2CA/C`/3:RL/Z92(_-)[*"LV?5,7^=[ MK-M6XMU(Q7A!0EW9#NX+@W88>7!CYOFA)N]&W9[%M&IBW7#U,JA]0Z;V#JR9 M'>PYWI&140D/..\X";RVP\3X+.V0;Z0=*HG:O^#:O)D3>&;5%(DUVM?Z((!; M*0SQE/>&G[#D$;8@<2M.\887!M*WTD*HYYS;,SX[\;VPIMJ>39X5!;D0=`I@ M$0P2C/*O*\FZ\VNS-5>6U80$,2Y`$&9 M7RLM%/;34])R)T@)HDGVF(W=V@,79Q%`ZX[5'U6P13SRNI3B'H<,$6Q:!3;4J*$\+)<&?!4%)R'BV0 MI^YN1\=!50GC14`H3@+.XF*:[C>@?X(I(\[MGARK2OQP,%UVZZDQF(^=C9$, M+L4\,*)WY!$T39%IS>$.[T$@)(]Z.VT`CYIKRTIH6>]Y%O+D2,7FD\`H[8(, M]@T9,'T\.$&W>R+@]'I'QTN"+L]>T)Q049FM7%T+@A51:]6VM"I`3B*?J#4'0\`8@-F&_JL(]AJP+X%.EL'F'6; M>,7WG6.8R![_!]XO'/GK=+!5QI:?D7L4CC,Z"$LOVV"%]O;&N.%+[EWV MC(/>Z%7JS^L/\S935J7%M#+\VCO*.R[JV$@:`4?*N0^C_K@<]+)S%36<%8]A M@32ED`\/=I,8RT4@3>*IQE](/HR.LL6;%NX%5/Q1,.D/5S/O[[ID(G!T5=)1 M(?M7@`$`217>A`UE;F1S=')E86T-96YD;V)J#3,P(#`@;V)J/#PO4W5B='EP M92]47!E+T9O;G0^/@UE;F1O8FH-,S$@,"!O8FH\/"], M96YG=&@@,3DR,2]&:6QT97(O1FQA=&5$96-O9&4^/G-T(-CNWO?C-:5P4`8(4M?)0)'U82VM)K:R5=4G@OR\/R5E) MCEL8\&AF..3A&0[)G7ZX*HLRAK9T65G8)GB;V6P_VUQ95[0AMEF93=]#Q@:? M36=7-/U^]25_.)B)=X7+MV82?>'SPDRJ,M^;B6OSCOXWM+:AL:)QP:/+^QT= MLH6%L/<0L[0[4^G"..P=5?@?5?PV&3K>CRLDV.:WQAB<<[.?J2Q>G/L!S* M.%JNO5B^04RT^1J.KMJQL%)!<+L3-,-" M?W1PH"76$`)[3`BJ+JI(#X0M(:3+G^-?+]LJO:(GPF^A)@,;4R9Y%LT.S#__ M5)'[49_,=Z:NA,F:CD/P0>PFJ*22+C40OG2$E2[9%",1\I0R%Q)ESEFA;(:0 M;4B395<]XE>'3K;(<".8,61KB1=R+<"IOL#<,@4TT!/%X^Q,Q$6J\J4>!<,X M-!!61,C"((AU48^H[6S9[;'`C/-&MM_VHDZUK@3(@XXS%1,]9Z3:Z,#N5_RK[F))'GHS06+Y:HSS9_=^X*SIB3B@X+Q)ZT$P>@VW?C_;K53P7@5[%=S_ MER8&7L%0'+WEYQ@='=L>5>P`-\F_;C//AJ.:_6%7;6Q/*.',3GSIQ-(CI7P\ MO/[2!75\1^6#D@77!PS9#8FWM+&^H.DBB)&L-8BMOGM6VI*3*"?TANC$%O8% MB^?8(B0-X0$!XH"5WP2!?<\0'8Q:(I[`W(LJ"3Q4+2M!1^%`M*805(MS/23Q M,B0=KT!C0P,O/$J]$6CGMN>&:9'7IO?4TFM[@\1/.KJUK.@PR*GOIAY%N00K M<^6+VF=KYI!^E:X6"G%/D6M;$/,-5V:-^2CI$'RBO&7I#BJ4A`<6WJC42QTG(=E^J6VK\R6+I\.SCDTK1*G"JTN-/7`_"/!N MUN\YUJDPGE-S*FC!CCDR-$ZXF1I?%A6G:B"CK%PS.3S=Z&H'",TXQ1.]E7-4 M>AHT%2:B$*'T<&OA48%B+6G1(V86^D-5X4H0%V]0R=SX9O^FWH*,0\G^@-]I MXR!=TK.V4Q2U49]I>NM1,@*&_1ECR..CS8:"H$>?YKAW@,R?R&%-\E_]WB'+ M482JHF1UK_K[I,\CJL8'#%ZM5&YT#V4C#'>B"9)=3AJ8N-STA)HO\0]/DR.W/\JV` M)#K!W5-*12<_Z*O%4R"FI,I&](*GLT]''C8S_!=M&L8W\_FN1\E#H%#AHX#) MJ!ZSYL^&OT3NJ,30"93<\I7F\B(?L`N2$)`K0Y6QRK? MZC976%0ITKA2C70D@L)GUIS@;'BV2/K']#&B$'UI8ZW'$HX9&^H2=-Y;G61J M-I!42S5\X4'WTH>>&M:G8Z)SDPSU%WFC;)LQ;]B4-]!Z!#:(0C_GJM)RCP+/ M/5NHT#=/G.:`B&O?(*>HS&ZOQ3IZK#V0?AKX,VL(\&NJC,!C!_C4].:'(NG].B MPUUV]VBC;?I2:61[7"(U3?Z$TLAIO9)J&:2,5=)46V[>>-ATC\@-X_SUMW/6 M9C32$??$&8&K4LT])1!;Q(IZD3(="-I#<_5`\XA>\)X_Y8"]KI*C`!J=B*"1 MO):^G#]L9Y)`?3X[R.I+G!,U^Z+R5WYL+/6AWYK*4?;[B(]6^CPU5:"!"GCD MCU0?N(Y75KH9_=*0Z-GPW0S\GZX+A=!*)^K1S:S7S[R5?>.AEU46?!:*N?]! MJS>H)EZ=ZV8J%'SL@"\?AL#C/-T1;VY4S4$!/CSKPBKM+)).O&K%3^36=/@) M+4M#H9%NO6:-/)N)?ETDBK-_!1@`)_CS.PUE;F1S=')E86T-96YD;V)J#3,R M(#`@;V)J/#PO3&5N9W1H(#$X,#$O1FEL=&5R+T9L871E1&5C;V1E/CYS=')E M86T-"DB)G%?);N-&$/T"_P,O`=B!Q;#9"\DY#F8."68PAU$.P2`'FI)L)38E M:XEA!/GW5+TJ-FG90`:YB.JMJOK5JZ67OUS]M%S&S&;+S=7RQZNR*+UOLV5_ M56;+IZMO^69G%E55U/GAP2QLI#^=3ISHVQ0Q/QKZU'EF?E]"F!=AKJC+JLY( MS`>6:NL`J4595HV([OA@FY^-ST^LQ>6L(A2!5BPML((VW^*WQPRK#H7-[S$G MO\]T/+LYX_S)8#D3:7W?'7&@42$T'4I:'[#\MC!>R63#&CK78N4*4[@K;3!5 M32?U`MD=UD3'H#K(^!#S(J&B$"\4EH4M*N\J!2?6<0;Y!Q-)=,FWL:SEAJX1 M;.')E%"]PMD7OHEAPCG!')R(>S(UG27KG"5H[].7G!@).:`0^)J1MC%T@1>& MU_,8;TSEV-LGE7-WL4^0674GD4\@E_09M3#F-7-F/?[).K+(T])AW8F(U7.6 MEE6*2CWO1^!/4ERC:`V&1069$+`,X1B@!/@$+2'!PQ MILB6=VO61M[N^?*>5IF?K/_!M,S&827J*&Y$:)6\F/^0F>4?[*9*W&2+,G@[ MNMU%N1CX+,PGD0TN M&H&HCC-H/(&[-`;-[H<=7,86_8]142;9D=- M.YT?#%^578DA7!F82L=Q:F9[Q0+(#=Z18S2ZRDL_S_SP+8<;'4CT,A1MT;BZ M21[1&&2/3,'V>):K8C#(_Y[_RT3W8!SGB;I]%9;Q(BQCBDNGZ:_O!D0?JR+! M[8C]&K>UB%A.`OQ[)_N`#&$U7SJ:LM"4Y3EMD"#)U"%)NAX=UO>B:5P08)OT M%;GL&*MIDMPPG$=Y-V3``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`EV`G.]]B\1G6KF91B3>TH4W]J#)8Y!>.9JQN!9DOA(];B1`+<4.36KWQC?2JIU4OFL])TT M^;>K#$+N'^USWZRV7$.5[K75YN/C9]9>Y^^_F(:=_Y62"'/TJVE`W;UT>@?I M?7:W^J>31/1@)`^)AR[RCKY1I)Q*C&F?^YMQ#4(^EL0`^LG`X%:\BC[#)5;2 M+N4&[EO#*90"!IJ7R&K3WOOM41L=[)R+V)B`@OQ1[OO9>-[VWD1/GR\F1KJR MX^3SU<2*PV7/1B":,ID]BIY`:3\3%;CSR.(#NT<1& M;3C9#50)BY#&TJG2FU7GN4>:'+=!$^/U.4C87^+0%K9LIE[=:>\V`>*L-$_. M(9Z`#8&"%ZSC2%LS4*^;0F(%29Z*9IV*YO@>Z0Y&<.`&(7N5`A:V*0*7[XL8 M;/S,P@4;9%%J6Y0!RW&Q9R#O$&(M=7(4]B"TKY'%7[TI0SL5=V]=>CA9T?$) MW4*5'TD"<@-\`FTRWA\0UHZ#FEWQ8!H0J$(IUM.#*:=I'I9>-C2G0+ ME(0]^E3I_#C>\&+Q(.0"E>JD&[?Z[5B'_Y6$ MK:_GT'=G3>>LF[BU>Z-O8O\E:*<\-C9WGXSC3I*,MDS=D\$+EP"^UW^IY/H" M?6/"B:O&1'5.6^P<^2:6[DJR;_2O` M`'Z'[]$-96YD[9U17])9^O6)#;ER4^RML$UKS9X^GZQ)<[PMYY9 MRZ[,^AHWV(_+=XOECXS$.0=0.>"8'Q*[_&?QTW+IDB)9;A=%E@=?)+DJ4+8N M*E`TK2CP,A"2)O-F)"U*TW?6A:PVS[;T-$FX\JPRR;^=[CK:HJ7E$P`U9M\] MZ8X+H+78>+U8E]/G(!<)6(+D!5*JF.Y-ZT,=D;F@IB4[-*0T&;7*G#D>94R. MAY&P>)8I,YTM<]IXM'2\,7$?#&PN>QOHAT"R0\2,NO\++W4'/4"S-/E$QPI" MKY,;V9I$+_'?LRT<:?;$YP<]$$&1%=LLF.3$JV<<]-.FW>UD)Z">;5J`/:,- M%0Z*J!=;%+/RI$;I1%519-SKC8/>F-,-T1Z1'G`S,Y8^";T,GR.]:5L`[ZL44`U+/-978CER>Z>NU7 MM%#]W[U?7RAV[U9[,J@L`2L'E9S9Q>E.I)%S\CL3^#Q,U,J=&.$WV+HV[VT) M%O]B0T/#'[;*S5\P3T$#;8#?8T0ZLC7"&RRKP`Y:?-(8?B7)$2HB%72#;SC\ M0:RZH;\K'Z(X`:E94>SO=>1K7Y,3<0..'IYM+8[@U0O+>T4B,=<;:5O=C:FS M2$LNN&EO\XA"MX)F+=OO@GP8G9"K3>0!TDP=`.7^@T2!J<<1\/:@ADC=&B@%&\:>#*) M^=0C%<$>--G+$'?N>:?>168==FS9VG0BACLK26VW5R M*Y*1R.F/'7NCR),JLN^^*-]5TT$N4<`*7Y59RDIB3N-Z95$ M7&FZGJ/":U24$H*5!+W(,M=1PJXTT^98C%:#'D,0D25@I(K,W_7KY*B'.$64 MF@(F`0$2F)?BDOX+*C(\U2A/' M1%E?-P)E8L@M&VX<+N/WN5U,/FQG&E!:XNO?H_"52$OH'I"6Z!PGIDH24X7R MHK5N&/J3DQG>,+T&$C1TX+T@6ZZ.+'NV381_?J`Q%69[4%8/D6I$O4U M7L$,L^P,U;^/X.Y8W(18F8HFME*D(>6K8W<&?5%\9:*WL%Z0NANX1$^+7$N= MY%.'?,A_$K2?R8!\L!,F@BC"Q&HJV`V8R%HO*0W6Y-K4MYP9J=]!,0>;[GXF MF#P9EU(V[^4!QX57]W?:S.G82^FCM?.TR,"O/,F=!$687@9%N"MY*S]K>ZKY M>>ACS^)";%#O^L-]R-?3`IH.=\BX0[*TU@3CK_&#G$B="&J>'T MU1S.E2:K/Q''W`2!Y%)&S&4$]3TW.,32$6T.958J+6PKCW2B`_5I13S]*AO( MZA57PQ"@'C4@E?3435PZB90#-V)@I(?31*0T+6*M>+*,JJ6JT5O5;$H-I^\* MQ9)"Y*W88]=K$='%3YM8H?Y&/]C.-9.'?3Q[[T_D;F"-7BBJ^H88*=)3263= ML!%CR\O(`QKW<2/SC[[U6=X4Q8UOY[ZJTK[J$'N`G38'!^I#OE!O0!;ED.,2 M(EUL&RV,[I?P/IIX?FNU:F**?_1]I1/#(EPW0I1D+;,;<2DWPD'Z?&IJC[I+ M-XG#Z1EQX7P7T`7DBO^25AF>YA>I'Z[4<6 MP*MKLM])JWQT5UZF+\EA")]=``P6B4B*L M\=LV3]5(]UPH_!V!NRLSN.9W!*$8OLY"`@]YSLF6&-2#_6G^Y2V\DI@/:13D4!8P; MO?TR+)0=OMT?:,R M<==0`G[RGP`#`-*]TPD-96YD9 M12^))5$4R>\C1>7)^MO3AW0UF94KT\ZLBC;SZ61<^ME469LFYM_U[T\_K]=% M8I/U[LEE955729ZL?WO*L]R6-+OAK[QTHNI74VMP3>92$BIHK3N3<$[6A4WOS*JDY:0? MMZJ_&PWMJ-(PUF-ZL\I)ZTL?-*AUX;1@U>[_K.)8K#0$I,$5WG$@5AR)$`AO MO02"S:_)OM[DI./KA88%:>E',MO2QZ9/#O3)T:*IFNT^J88?B?A7_^$ MP_*FQFD*7HP6[=A2L-CU(Z!TK`KC^1Y)G_FZ*:Y(%DU$LA2]?YT/"$3-]I6. M(C,;YQC-XP61J06:FNRV%-7KI$C-NON(U26F99#9ZI;C)6P2X#ZF0*H*!^Q5 M#DBXH&MS[CF:6/EH&#P"Z=[FZXG0U'>B8JMH:A@6:'(PVBH$(Z\E&,R1G!)B MQPSS<,YQ@API36R:=,;;R/*#K@U$O#*GF>P'.-K<+G'?3T_9F7=^"9B63`%-SBA:*PH7QO/.=`9"DJ=?N[E'X$D`P^22B,,]X0G MS38$:`[0BX8KP^1#%\)WB%'T&ILW"0'3UCX$.B]CH&M-^W],P8'>&\<%B;1Q%B8K^:?9 M5@I/P?P@,]E(GDJ0`.ZZM*KD9^()Q)KLL^DKY9YLN.-`?L]AYQ;<6N][SH_J MP2\K;L4RX.'1A_3['K6H37M8<7J#`/EV-/X,][(RE.);%"+J6'4?>+0E%& MAI1.&<)FLI%ROPJLY&D)+]E'XF_I`;'DU\RYPW0ZW6P,E1*WS,2L\&'UJRE; MTN1=F!CY>\,RA.@[3C-W3?Y1U7-$F8`D\XR3('YFK_F:Q;+JH(1%85--5%VD M3./$Y;9@;A=F]4X,LXWGPL'F;GGS@<\0KK!%')4.!@V\()&FXLE,;6*-MEJC MV6O:Q'XSALRJ`3ZVZ6&'\M.D!VX"\(6(T8W336"ZW$T%&$57)SE*(RZ,.4C" M@UD&/2LFDX&0,L+:(#KKB7L50(B_4,.!'L9X+K*D_E66@_0K)B596A3Z@NTI MN8QEW*W4CYE;9<2SZPW.39>3YM+B/BG=0QTA MT.K<+Q+[X2HD_E-`AT%Y08E,YGHIN[7ZG.)"'$"2(4Q+'<^E_15I[9&@G_\P9(CSCX"7V==QRT']&DHOYJ"HZ&-JD@\+R571X3NK+,30TT@ M=.'L/EDHP/^$HHIH8TP=.#K-`G4S-#S0/:HC29#=WWDFA_>)=/.5CC=\0M0? MSI78C/@--ORB![W1`:)3JZZ=6B$1_P.UHJ*86E1`I92G7VHG"&CJ8,ZOW(92 M3KWG3JSBDL?+S%,F<`&C4$$IF!ZQQ(C[Y_0\&7V4W69^;$I#QOO07*WU,A0, M+8)0X=*14MH+&@W@G>&QU4B2<$+,*+CWD#A9?>XX!4&J8P4O1'T8WV!UW792 ML8L>,*O:R>3Q;?!HQ$F_P".&"J/GZRS,[]2S:,(8%/1;_9JBAT%)>&T&^X.A MF<1>E_]&B0][0DQZ=,?+BVW1O;O02J'WEOZ5,PD--5"4`L_9MN]>8E./!-/V M62>A0;O_BZP,HB[T]R^4B/BZA(UHQB?>$WVDVN^UG%2HN\2+AIL"%MVKD`YC M-R]M_*?EFR.-UJ_X<3B('CUR,X7Q\RUKA%%?S+',M0%Z^16PEN`]%%[ M5+*5WJ$+6%46[SN+EOS]Y6%!-@8%G,2M/`RMEYN'+R(BK9=[R5;B=?*?``,` MZC#;1`UE;F1S=')E86T-96YD;V)J#3,U(#`@;V)J/#PO3&5N9W1H(#$W-C0O M1FEL=&5R+T9L871E1&5C;V1E/CYS=')E86T-"DB)G%?+;N-&$/P"_P./G$7( M<%[D<($])$@.62`(@A40!$8.LBW9`BQ12TFV]1M[R/>FJ[M)/;V'7$1R--/3 M4UU=W3/Y?//C9!(RFTWF-VU9)6NS*IO\G'[]G1\I;6#_:SN0YTZD"?O9K")IHZN#28N*=O+^.\Y^#9WA0- MYG#7>E2UMYVQ.QZGIA]ZR MNYDA-]H\6_?&X>C=TC2TW5JWWV*6SGD`*$"&QMG.W`0<+MMW^&#`<":'2EL M2R"]T&XM)US,5SIV;P0^US+).''^-%8`D2G(3P=7'45ISMG6:K@0B@U9\!=, M:,N(3*B^DQ5_2U8H?V,8^/M.MJS(R8!3Z+/7!/B_6:0)U%%2#*:&M&;73WEC M0S,(7*S%?^*@1TZ`@Y&>,]ZPE7`A>$6,('-$:'\S3EC`CVRO:[K=>&C);.)# M8@E+)1+6"N?)ZV&W3L?X#+L-4\1R@I\ZLS2D#V/!%DN MIS)`M$5L'^2101P\IVD1JI)9S?,)>U_3=$+?AF-VGN2,C\U`RKJ-LO&OOQM/ M*I;__(=)GKS]8FP5*6)?#%4",K0&^3QR`H@0XRI.*";>TA`\2*8@O`N!RQ-/ MZ65P@,2BHNW%B)J<05K!'DJZ>)%/U5F9L6X4LJ!\G.S7'$Z8(*V-NO8RU9KX##\2BP`L$E/"!8S569+X-AY5C;NN8W^0 MQ7KXTS,Y63MJA`M8?9OO9YN/AF7]?$-'\M$?5LJQ#J@^KU`D3D`3@/C%W/>V--#"&VQ,B M1SS6&#IY.->85G=?K+A1:9&7"2V1\?3QB(9*WWNAVN5Q?+3A4']]'$2K3A*4 MOXQ%C7SB8'=:35EE55:SU6[)PA_S.YXTRBW2&/QTUS*J+E-KVU-(AN[A'2@^ M&8M'E,&A:%>"R!DRR0LR)*EY5NHS1AD3$/F.JQ\G=926TR,[-@K=&2;-:31"Y:Z@4@LJC:`2 M!)60.T,$][F7_TK#E;@=V<-MUGF%J@6C?DKT<1"O1Y9<+N_U%7"2;](!G&0/ MO5HK/FZX+XC4(7G+70D_='"EXH(.(@Z#60^'$\XD4P)&'W7JC+.2KP`102N' M1GOVJ#/+*Q*3RI0R_JDR[ZE#S$@&2XC%\ICDXG(A4KSFG:1W:>1F0>(@5>J3 M":B`E@I_(87?NA^@TH`;TR/_%J+.K>9(RX,#2ZD1@Q(=18!O05:EH.=>`.?F MM@.M0,C?U*?NT3'*?N@/'6W#JH^2#I'G4JXS>W2= M%!:=^:8U>#T8V&RXMK,4C)7;CQ>@]70K?VN#H&9T]>H\6(4_).]1J6K\48`V MVYZWX@L<0K7B>Z*E4_@KH%`5L*G];A_9:?OVP!WC:CKH%1-AS[J@/2"SX&WL M"PO/374URO*QG!WNM[<#3:A0@T6]46HY3=J14M]DWE:V5N%\VVIW^:H'93=U M\`EI@P)C*^C+![3!WTZ[T0LI/*;[8NCCYPONSY]GEP#&-AS5*C<"&%IMMB3* M[,L8^6Z.CIF\8"+1.#9`5^"4!9=R5^A6I_X2>8_\11^7F$]*=XO(Z&PCMYU[GM'QC-Z@ ML24;^)!%8[],GJ*Q8!-J7*>_X:9",^>&+ZZ#*=E%EM,-]U$=$^-J3UT:G5:? MKF443GXF--KX#*!J9D/OM/@`$`&('5L0UE;F1S=')E M86T-96YD;V)J#3,V(#`@;V)J/#PO3&5N9W1H(#$T.#0O1FEL=&5R+T9L871E M1&5C;V1E/CYS=')E86T-"DB)C%?)DJ-&$/T"_0-'Z@"N%8KC1(Q]\'7D"#L\ M/JAI6JT)-4@(S?+WSHVE05XN@BJRLC)?OERT_W7WTW[O$Y/L7W8N#Y4O$IWL M/^YTKKV!W7J7P:O5,=E_V_V9OBAK\YB>519RGW:'@5]._&A59HL\I,?DTLGK MZLN@K,F+-(%EF=Z4]7F5UBHS\*GK1]ECHFR9F_1-1?@]*!OFD[W*?.Y&M=^5 M)FU_[PZAQ)UFXX3@W<"Z"EI:TE1@KTO8"MU08:-GO9?T& M\FPHA0(L@ZB"N>B5![FFE9>:2!3ENY#D\*Q`BTN?10BU@M)&9&\$?$AOR6

<0X,@)P!HR.RQ>'%D^#+5G"CG%YJ@C(2#"7#$!&6'!18 M\OD]V_0_\&S*>D^8(NX'P4?H,W*O;VYKGK@\&B@<4P:%$20=#"O^I8$*0A7E MWBOK)%LPI8?#$_GLB80&XK;-$-'_WG)?A(7EYY-4&F"@`Y-#(.:L^)R7VI8S MIRT&ED\CT(XB82D,!6#!.O#]`E\-9O6IDS?`WV/1H@OMMC+)56NP[<+D6R-I M<&[J@5+'4@HA!EQMW+9806V)E9U+=RA'J$TQ\I'8W2@'YIT198L+#:MZM!_* MF`)Z@-W@^<`RX"CZ"VYC4<%<27GG(D>6A_DI5VV<%R-7SB^)UA&9D%1(@N'E M1#P/`,666Y!^L\-%.55G7SI6=I$"`?48XD=A>>6MA)J)04>P*"<'559S&?`5 M-1B2./.CV0ITO.I56<`J:;OVIJ!*>):]JHCG[GP!;;7\7JM@19]<+T)BXF7< M)/6#*L,C'HG[ZPY7ON/153*UDUIXIUSS&_XOL>1J9J9JYN?`!`C)G9*RD,K$ M&;#:]W.!?%):T#ZI<6O;`3RFWU(K]UD_QTJ"7 M8!ML#UA1S,9;&!_*Z.=4*>:^7@ASWE2!=1]92!2@2)R(\$!%%>(TP#CJI+AS M586FN-&#MEHZ7RLGZXE`!,U)Z5D[?Y%#GP><`C0/`18C,_YOP#D"8#'Q&H"T(+M=\53A#74+[(P M3FZ.B%-P=0_$$R)'TO6879`;-Y%K1>[X6'Z<(\.XQ(".K]Z. M6R[W.LQXF[G463^EI^-RDY&YPT7YY1*]MT2O@K#C)A[&#W>2[J>O%>.*U*(N MK!%U\W!(%=M6ONIE"S[VC-/A@FV!:G#U("W!T,5_#Q/,-"M(,T9\,@3LY;_NI`:^8-P M0PS`;MGFJ;4:YWPOH]8L]V">W_PG\68!U'>B>)'^./:,5<%8%0]*F([PY^Q! M\RMG1D@#DC;R;[T%4NAYT:B^GEAZT:D>][S?5<3E'_P`/(.?OQ[P].55FJ), MSF+X"@2>-8G00:9G:`J>*VM).%7]3+LY_-V@."C0".2S1BS\0;\I5H.O` M5[=RQ0_6DO`).3YY(AEJK75,`L`C=:@STJ, MQ185%&*D"0`#"B`"$0`R>:TN+3LA!^"2QDNP6MP)_(N>7@>0:;TB3,K`,/#_ MB2W7Z0T`0!DX!RB4M7*<.W&NJC?H3/89G'FEE2:&41/K\01QMC2Q:IZ]YWSF M.=K$"HU6@;,I9YU"HS#Q:9Q7UQF5.".I.'?5J97U.%_%V:7*J%'C_-P4JU'* M:@%`Z2:[02DOQ]D/9[H^)TN"\P(`R'35.USZ#AN4#0;3I235ND:]6E5NP-SE M'I@H-%2,)2GKJY0&@S!#)J^4Z168I%JCDVD;`9B_\YPXIMIB>):'!P4)_ M']$[A?JOF[]0IM[.TY/,N9Y!_`MO;3_G5ST*@'@6K\WZM[;2+0",KP3`\N9; MF\O[`##QOAV^^,Y]^*9Y*3<8=&&^OO7U]3YJI=S'5-`W^I\.OT#OO,_'=-R; M\F!QRC*9LHFKZZJ-NJQ6IU,KL2$/QWB7QWX\WEX9RG+E'JE%H_(PZ=, MK57A[=8JU`9UM193:_]3$W]EV$\T/]>XN&.O`:_8![`N\@#RMPL`Y=(`4K0- MWX'>]"V5D@2``K`4R$$YT``]J`&H1W0;NCWT%'H!'0.N@1] M!4U!#Z#OH)U%A]%=Z&'T-'H%G4)GT-<$!L&6X$4((T@) MBP@J0CVABS!(V$GXB'"&<(TP37A*)!+Y1`$QA)A$+"!6$)N)O<2MQ`/$X\1+ MQ+O$61*)9$7R(D60TDDRDH'41=I"VD?ZC'29-$UZ3J:1'0/R5?)M\COZ*P**Z4,$HZ14%II/11QBC'*!I^ZAGJ;>H3&HWF1`NE9=+4M.6T(=KO:)_3IF@OZ!RZ)UU"+Z(;Z>OH']*/ MT[^B/V$P&&Z,:$8AP\!8Q]C-.,7XFO'9%YB,6A>7&DK!DK%;6".LHZP9KELUEB]CI;`V[E[V'?8Y] MGT/BN''B.0I.)^<#SBG.72["=>9*N'+N"NX8]PQWFD?D"7A27@6OA_=;W@1O MQIQC'FB>9]Y@/F+^B?DD'^&[\:7\*GX?_R#_.O^EA9U%C(728HW%?HO+%L\L M;2RC+966W98'+*]9OK3"K.*M*JTV6(U;W;%&K3VM,ZWKK;=9G[%^9,.S";>1 MVW3;'+2Y:0O;>MIFV3;;?F![P7;6SMXNT4YGM\7NE-TC>[Y]M'V%_8#]I_8/ M'+@.D0YJAP&'SQS^BIEC,5@5-H2=QF8<;1V3'(V..QPG'%\Y"9QRG3J<#CC= M<:8ZBYW+G`><3SK/N#BXI+FTN.QUN>E*<16[EKMN=CWK^LQ-X);OMLIMW.V^ MP%(@%30)]@INNS/E1Y;/;[TA#V#/,L]1SPO>L%>P5YJ MKZU>E[P)WJ'>6N]1[QM"NC!&6"?<*YSRX?ND^G3XC/L\]G7Q+?3=X'O6][5? MD%^5WYC?+1%'E"SJ$!T3?>?OZ2_W'_&_&L`(2`AH"S@2\&V@5Z`R<%O@GX.X M06E!JX).!OTC."18'[P_^$&(2TA)R'LA-\0\<8:X5_QY*"$T-K0M]./0%V'! M88:P@V%_#Q>&5X;O";^_0+!`N6!LP=T(IPA9Q(Z(R4@LLB3R_A\0EQG7'3<1SXG/C MA^._3G!*4"7L39A)#$IL3CR>1$A*2=J0=$-J)Y5+=TMGDD.2ER6?3J&G9*<, MIWR3ZIFJ3SV6!JF;TR_DR'(J,GX0R8Q,R-S)/,O M6:*LEJRSV=SLXNP]V4]S8G/ZU'&VE M]G2U?75#]26=EZY+-UD35K.I9D:?HM]9"]4NJ3UBX.$_4Q>,[L:5QJFZR+J1 MNN?U>?6'&M@-VH8+C9Z-:QKO-24T_:89;98WGVQQ;&EOF5H6LVQ'*]1:VGJR MS;FMLVUZ>>+R7>W4]LKV/W7X=?1W?+\B?\6Q3KO.Y9UW5R:NW-MEUJ7ONK$J M?-7VU>AJ]>J)-0%KMJQYW:WH_J+'KV>PYX=>>>\7:T5KA];^N*YLW41?<-^V M]<3UVO77-T1MV-7/[F_JO[LQ;>/A`6R@>^#[3<6;S@T&#F[?3-ULW#PYE/I/ M`*0!6_Z8N)DDF9"9_)IHFM6;0INOG!RAMJ(FHI:C!J-VH^:D5J3'I3BEJ:8:IHNF_:=NI^"H4JC$J3>IJ:H_R#W(O,DZR;G*.,JW MRS;+MLPUS+7--:6YQ_GJ>@RZ+SI1NG0ZEOJY>MPZ_OLANT1[9SN M*.ZT[T#OS/!8\.7Q=O' M$IKL$@*!$$!F";N!&.@D!.AN6F&7?#2AA$3(4%*%IH4`W4``L8+8@E,J(ICF M25-XS$@'*TQD0%N*2`=%4*@"DE:9%JK(/G_O;4JATW'ZA^,[<_=\W'//Q^_< M]V:)B2B)6D@B3V5]J+'CM\NF$,T90<17*US+QTFFM>(,Q-J84C*3#A'E-@$ M?41M?=/*V_L3!T'?`?W:DH;*T,[*MAJBLI]"7U$?6MD8MSKA5SA?"EU9&JJO M_M/I3,AS1Z$>9V/#\B;4B6=NG+G?N*RZ<>FM;TY#`RU$\6?D6DK'RL"R2YV4 M2F2S`S@):R%/(QW[J@ZB5]'=^G&JH@SZB-I%`]>2!MYO&(5XZS:-N MQ\U2H;03.X6@]^@<]^5"H]QXPSB)/*.H`+$"M!&TA7;0:W28>BC".5S&'<;3 MQC+C,#F1JY:>IPVTG5ZA7](_.9O=8JQH$)VH+9UR0&;L^:CF9=1SG"YP`B?Q M?%[*S=S%=T1`.F0T&KM((-989#Q`1^EM.DEGZ#H\$SB="[F>NT6'E")MDW;) M*^37#=6XAOJFTQQ:#H1>I$[XOT\7Z0K=H4_1@YU3.8/'*4YZ13IA2XI<,?YHW`8J(RD;&(]'1"_Y:!9Z-A%7*S\8B19^2#?H,>)"`_!"B-IZ_15&MR3P+-6GH:F==0*ZT'KNVT&U/L MHA.HX"/Z!]VBC^DN_9LEECD6%20#(95'82IC>`(HGSU!;F-(\?1T45 MO)"KN(6W\G?X,.@M?IN[^<]\G6_Q7:M*621B:L6B3)2+56([Z*`X*V5*MVS# M;=DVC^V"[:J<*N?+%?)+\H&8^-@W[]V,=$2Z#)LQRV@W=AEGC1N40`-H'#V& MMV`1>FA`#TWX7FRF;:#MH-W`\L>XR8=PCXYAQMV@4Z#3]'N@>@G3NPKZ&^Y8 M#WK\%/TE`.,HF1--M29:P%/9B^[*07ZNP=UHY&=X%:B==_)N(/\:[\/-ZD*/ M#]([?!GT%[Z&KC_FN^A[H,@!S;)Z?D(\)UI`K>)[N"$=X@3HCC1(&BO-DYZ0 MFJ4=TC[I)](IZ0;F6&,+VW;9WK*=D4G.D&?*E7*SO%[^@=PIGY;/RM=C1L1T MQ&Z.W19['5.9C]D4T,-/"F[8#^GG5"M6B"Y\$8:3#>]Z)S?1OT03)'.D>HCSB4C.'#TM-2A]J'#!XT,&5`_^1^??LD)2;$Q\7&R#9),+E\ M:E%0T48&-=M(=>9,MZFK(1A"#QB"F@)3T<,^FA*TW)2'/3WPK/F"IR?JZ;GO MR=6`HO58\FQ+WF+)?2`['#B@^.RU7D7C MH.+3BE;4AGU!+\(=\:#U!+<+8).'$LW`&DT/K:JU@YD>/BU5]?JTH:K7VI.< MOE"55EKF]WG3'(Z`VZ7Q]$IUD49JH=8ON_>X>4Z!ZQP_'`3F-,=_ M,-63ZE-#WH!&I?Z#0SU#+<7M.F)?/=D!4(ZXI[FGF7RRP[XZRO^Z)FI_[UBB MY7?\,GC)G/NXL)E)+4:9FE)I)5%1ZT3SIWHBA2LGP@U/@-%EG18_/1A.GH13 MFNQ,5I7P)X1!J3TW'[:$>BTQSN1/R!3-<=Z_$=COE77*=)7H%%_J_QES>T!G MHU4G[[`C%$_2P@78'F5>ASHO3D-YU`5#E@-2EDLI0M5%YMR4L!(NK@HK14HM M!FYS6AP;U>%`#MHI]]?A=Z[?H7D":??%ZD!@$N)DFW%L5IQP`!$6]T98;$5` M@'MP;P"0X/X<*_5KQX!B(``O]_U*P5?5V7MK'HV: MW5D0GW/^.\-@'$1Z':L=:".?]CQ`>_U40GO"5$,[_ M]NT//1,BBD@IX`@]M," MK!P;40/TQR!7F!SZ6BP5*P/+C96+O3VVS90K=Y-3GD\.PYTARBPSE@\9G]4 MMO(OQ]GEY(6_F2M/?+[GL/(0#3%E*9/BL="/T6/6B]N6C7,O"@]V%A64#7)9E%WCKLB`L ML&:!AX+XY$,C$5U=*4*(&HRZ*L0ZID63\0,:$DO'.J:CU$*F+:UA'XR!Z-1D MM),FU38?CLDX:<=)B9W.:&PZ3-I$P9Y[W[9)9^@?_:\[<\[OWG=^]YYSS[U[ MWGTXNQR_%,(OY>(7:WQ<.^R<";2)ZX#KUAFN$_H/N2=`WV/Z7<;X/=<%^A*W M&?2K3*O,%YG>R3T)>A6T5W%;8!;"V(3;HF"#5!//E>*K*(($?(7I,:9Y*24B M7(T(KT>$5R)"7T1X-"*4180:(WX/[@\"CC+=Q;1;BB\7?EHN])8+SG)*^3-< MA`6\DND,IM.DE)`P$Q+>#`EG0D)[2&@-";DAH285]\/G@H"?8_H0T_N9WLKT M&J9%ILV2.5_X*%\XG2^\G"]TY`L5^<(%G`177`$;I<1)X4^30MZDD#4I3#XB MO([?04DX44E"<=/X'0S6K$=VD"G\I1*V`1B%V`'RGB!1C^H0HW5+BNB!L` MWE7$?(!KBI@#\%L5?J.(60"_5N1L@#<5V0WPAB(7`EQ29!_`!47N`)A2Y!F` MUU284+S;`13%>Y!5<)E``>4<`6I\>)GT#"+ M<6]L#7N@?PHP`DC7M@L-,OM.-,CL.W`WZS\-2.U/X6Z6BVWP#4K';8$U4^Q4 MQ)7@IDT1%P&$%+D88+TBKR$U`EZ+9#;9XTAF$;8@F0U:K7C'@+9*\(7\'F9VFAT`AGXM3V"6ED;^*,^0S<3&Y*Q:3.Z*1?.IUD@\' M+]!(T`?`R+:2#T0S>5^VD&NN&7(%SMOE\&GRAMA!+L$!>56:TF(IB?Q2+"6_ MD!/(F+R=_$RFSY+)CV#,*7F(_`#&O2!N)_TN]?DAR4X.PB%Y!N;9[)AA-IG=JC%K;=:@V+J(5MEUJU=JHUK$TM5VUJ??N66LK:)NI)O0^F.T^6 MR3FD$CR-*21(@U5(0&;N2[Q3-&E%PS1I?K+(FT^(;"1KH_PZ?@GOYTOY0M[- M._A,/H-/,5@,)D.B(<%@-!@,>H/6P!F0(67JX2TI%T'=2M&;*.BU5&LYJNE[ M#%YP'#9P:&6-C>M'!NXHR&&0YT$.@?2!?`?D`,A^D'T@O2#]#V]-T-'37#]W M8-*D-@]P^V,/]W.'8ZW#W+Y8:Q_7RUI3@-0G8'0EHO>8-A9JAAO(!>XZ>Y,JZT MKG::\U,(K9_&N[FRNC7T.=Y=&P):(Z.A8B$1&$_5&2H-#P7BX&TDP MF20Q5GH2[J8LW)V>Q"9+9?Y<+J#(+DJ)>EQ`B+H\S)SWM=GK8.9NU=RM^L!? MVWWJ<(=J=X#=\__TZUKZOXZ8&+AU;(1^AK4[Z[I`VL<'>N%+LZ\C.SMZ[%;L M^\S=WM&YE>+FKO%;SJ[:\6/.VNSHP,@"YA%J'G#61M%(W>/KHR-25ZTR(`VP MK[>)YK.-Q__#U[%_^VH\N\!D9^EDC=17\_$%S,>IN9GZ.DY]':>^FJ5FYJMN M6\O2/=_X]>S=JS863L,>>GOED`MNN(FZK4B#>%0C9>CT!%X"6IYHD%&G)1H- M9X_3\P2C=`-4L<()QY;5\-=IG@TVS06;35\$FTQS050=G`M2*2XJ,3O,>2`N MW5_>NC^JV_K5R;-C_*172#R(R"4K9=;S=R"4*R-D'0F(7DY+0T MN^:<8:,YW9)\W]&RB7EHFIMMKNNJO8VJJRV!``8I+L*;+.5E+JN>UYM-::EI M5G>>6]/6>Q1;1TL?6U,Z\MZ1,9/&_L>'/PST1)3Y3?/AB=U[`MT7[^%&Q`J; M#V)8"C$DHZ52K@$;S)Q>I]48$R$!26:=-MD*<21O-)Y+3$^QWG>L?T*-8W8N M%D>0!6*VI+%($,_K+S,;,ISY_FU::EFKJ+_.4DQCOHAFE&<>/197#1_ M<;!N;V!OCX)_C,].1'H"0U]\,C^CQK.32])\7_<]U("&I.Q07*NKU1-:'JI_ MTK6MOM?U[?H3GE<\YST)A56V!'\#W)B73XK2TKXJ:$AQ&7R#!0>KI)P:(U>- M"I$-M`7VLQI5H02N6C([_):F/'+.4FQ=5I%TKD[;Z+L1G(4]"LP%;U3ZKM@? M7'E@`K'93==1]6RP\H[-_K$]6'G7=L=TW72=+A!#=OVE926+(=/EI6HSU9JB MMZ958=;2\M;4-/K$F>/.X[.P-86G32#Z2]T^#-EAG?(J7(Y_Y__5]H"XPKNZ M,7%==8&[UY#`/R;8:[VE+1R7M+8GX*M84]VZ MW*NYF4XLZYQ5]7UVOGW(5UY<4>$\T6D,3"SQ;!3=IJRTI'#!DJNI_.:77;FV MPF7Y!6<6QYL3X@+18&[@44YC<=(\_V1^D,O`EGI]LN.'?\ZAFSWF^[24SYG+BEA!P"9WJ8I M2H;=]Y?FN9TYL86SO/!Z/KK)UV*,3S%FZ2M#FQK"/<^O.#)_02IJ66D5$G2M MVC1U8T0VP;^RO_G-@#P M7O(E8`-=BO&`<<@X8KQB_,9(XM,MB/,`TL`&SP`9/1.D4&U%M0\8T3L!AP`# MZ<&=QOU&S)B&9Q66)7#<9B:MQI,"%,QL&CXWA!\B("'8HV.74XB+8REMN!W) MKU.9A_#K2"0>`ZF:BNHJ/H$012A6^2MYFU!IEWK?7NR+NA)2$B/EQMU9$%_T M`FZ?J_"TD+@U_J/GGXSG>TB\"ZQ2AEX-Z'CH$2E`P"W@WC,W7W9F>'1 MX(/Z['!]-I5$>[35DYS[&JS5.H:I&J#1(-^S[Q'&>FB7*JIK*G')!QO:]G9M M6ML4*IXRX[][^OZ][F7U-/3M347C2Q_^,0I7O''Q-\^^.R<\\\JY4R?;+VY2 MK_(5Z]3F_)F*)_Z)_X7<@D;\#\H"NS=8/$4_D^JTKG%V45W6C<7=WM?U/?;7 M_/U4OWV/]P`U8K<(HH?RT!Z/1ZKV5$O5WF:JF=[CV2,9[8)@!W@$FFG)(]AI M2L>78^@A0J%"O)LL[PN9I#3\1*'E#\S0?'=^(2S\$WP?T)A)H3\@(7E7CD5B M400-=R.3RMQ+95+<'5"?J3_'9;2)0&.11!_1B#-FAKL)%6BS4-VP9YCL#Z MT-@M4ARBR6JSH&_-UOA;9#AD^,APWH`;T%/94>='QQN,A,^R?<5I M;,7A2$ET['[F#J=J^I>ISUB24;22CWU0HS_0)'[R0$@)[6AD(;K1UJ!NT@]` M907@.5)'8K%I.M*,=,HN3V]4%K:I\N_6C\Z@2USQZE]?A89CGT!&/3^!7'JY MQ:#;UMJ^?^K,@/+3WG]]GAV2FGJ@56_6,3=/_@-BZE_5;]7N_YP1V.14&H+7]&1OY3]\)%L(MS!16(IWIK+4(6*25^LPXLQ$E(ZC#(@ MFM1REVM!-'LSBPA@EZJT12P=OT)$QJ_`@0L7X/%+E[19Q[4L1OZ<[$&5C.HO ME%7;;5!'ZY@PE:1JZ"8XFYI-=]*K;%VV7O@&M8/N->ZP[;"?!A8,=Q<8*!>` M`LT(=1:&H7=R$QQ64&8Q&"C*8"B0:0IBA(\16$Y@#`6$FX#8=1K@9:X)-W2G M8;^"]``GO#QN%F4?QQK\N-_/RD'$AN,*NY6[Q6%<&MX\XOM(/H&M`('H/?>- M^ZD;[L\0Q:.@'GEC;6W6H85`3=LSESHB> M(X>'A_4<>LO+!<1]N,:9&E@)BQ!KI2J-44&4(B1$(KM-"WL2Q/W#_`FUKZFL ML!J.)N&9>7-G93O;ZSF:3ZB),I,XS3=+?08["V_#3]6`VDP^$=Q.+!\?&^S$ M$@G"7>6,%X8WO^B?+Y?:&)A`.&N8(WL@_H=T0D2(Q\$^I5EGMIM7"CVF5\PC M)IW.O-:UIN1%UV?"?>%!B9X(`5&493(DTK*/B(4MUA@I^==$X^_$(!=38L_' MSL>(6$RDI2A#8^&HVRT:BM)P_7&6+7582Y^_F\"MGE;\5FNQE4R4S+^PM=]F%1(KA]Z[A(UOWM?U3F2*FLB^Z2K=M^O3 MQE)'4A MD6GQ`1=TI;$E@_8R5B,=MD2I*BKR\B8^RF#>:``80G@H%"`5LRB93"Z_(CI% MR>7R%RM^40KN#\!E@?6!G0$\@$`\5F(KKB,1AD=*&L+1[C'G0PW%5&K,Z481 MUJWAYZ[+UKJ=DU7^$DH;8U_6?SFFU5LRJ6Q&BWB0J\V#6UGU'71Y7SG,@2D@ M"\]MM"22\W,H+?8GIWE;B+S96RVI^([^]Y!?8+_F]I:Q_BBBU>,60Z$G# M`H7R42+=8109)@TKCM`=NC2T*&Z\'"\O+_,'`GX1%SR2)/R?[FH/CJ*^X_O; M1V[W7ME'[G9O-[F]O=O<7>YR69)<2"[;8J#(!0& MQXZES%2EA1I%II,9.DJG9:R5,`E6&:L@:#!25!AKQ6EM0__=@\?1,Q!YOEVRX:5:S%Y>[U MYHW$D@MG@(9>@EX_TV$;D!.)E5;JP8$R-[&AFJ5Y!+#06B$JT>:Z-1P MD;1-:6U\VB*M=;*%SSK@1'47&*AU$*YDZ5<_Z^M\M5JKCU%N>2KJ6G'NE-)3 M]>)PIE'N14=61%K!E>:P@8ZM4)ISD<6%3CAWIM"FWE68G\:Y4`]V:9G,4NDT M`>_-Y>!PC\R5I=,.3EX^K:P(<5C:'D1PT8SWAE@LC2`EWJ)Y.'-^Z)6+]9HB M6A9"_AE=8^*2#YXA&K@?XN#WD3S&!RP0:)Z!((RA]R&"!G4KD_V'12FX?KCH M[F];L1W@@;(LVC9'[4/'^]5L?W\A#>Y+HURH%[O4*W,XW%%6[IM6EK9:JFSO M)R'"_0P@/Q@).,M;))TQ`)VCO\O``9>%/4_9)2+@`!X0?Y M7?SC/&X+K51.#^.62#POB3-":XP;4"%$`48`Z],S&IV?M&P*E(3@EN^W1G>& M]4KU$C77"I5T?.>=G6O';O1F[[RQ\NNRF<;;MD]G.FH/39JSX!HJ$<2Q$JXA MAMS4:ZN<`*-@Z0@Z98X2795N4>ZD=E/.O21@6B2/:E&95\/8/8@4&P6\SJAX M7"+5"-L"MR42_J44M0!P1\(2B^$QQH57*:,W?Z*GG'(P!(MKB@T&JUS4?AG( M(34$0L,L13E#-#@(*S7T&5+YH\4P$1&QIA<^5#]R^<`V*@WT,^!F* M#W1U#126]_:5F\YFDZ"Z'C:5-%BT"!M?TD2FI[NPHVDRMW5ZZZ;;X?1@S0;V MR8TN_.#TW6M6$FG;U]MO7B#^!:?)"QN`C`SIJY^27L1?)$\R;W`$A3M(DBX3 M*(FX@GQ*7"8ONZ^77V.N<5?YZP&*1$C"03K<9719!250E4/,$/=DX$GI.'V\ M8D08J:3+M"#FU?R4C,DR*U[%KCO19=A:#,7Z())K=4I9[AQPHLX^T5)5)60E M:(.&AU'R(#MQ`L-`-ADJ-[N)1B-AS,HX;"/"^QD:EB)++&DHK1$<65KWZK-7 MEJ;J[KH"9I\]?_XM\TUS=.*5-\9!.Z@$S/Y_@D[097ZV[[//]YF?$QM.GS5? M,E\Z>_K/;P$5M$_\J1E3QL&E):C:[T4.)TY$3H'7N5,5 M9VK.)"XFKM65.P")DW#]C@H'S_,Q7Y1?']L8WY#86K$CLBVUI_8`-^0[F#@& MCN/'R3'Z6,7Q\%CJ)+@,/L&OD,%`5:6B!]Y[R%NF:1"D*`E'K(K]R`\6^@'M M!_Z.J!Y5O%[,>0W[SS=@JR_!EK1@JY]U"VPY31P7H1M!IS<,@][YSFM"$4A: MG!;/O@-+YR-6$_G_<#J"P.(P;]<1-58'K*)BX_M->&_T'ZE]=7.\.>E>NV/! M=XZ8(SI)!A[>_.[KXV#NMZ%]<&))\_ M$H>@#H20)')$-WJXW>R0!ROS_-B#8BV(%%)5O$6BU(C4(LEJ!)/$$!Y+L@&! M7\\!CLNQ@A`(2*P@<;R7\XL!-CD@SA7]L9A&H2%9\$L\&>GS\JF$-(QC4.I> MF)?JK(6!:(O-X?<^L)S3>A)>N,1D?6(J^E@T(2 ML63<`K/(VZ^R)@029G,KAY<(B]@9TTY)RD!7*K@.W7=VU]4?KEP'#C+12M,P ME\V>M['0A9XYHF2&%C>FB8[[L3U;58%*)Y?]]=G^>16%,:$:%Z+&'W1='0Z4:<')'%UI920X$7W6R_G)SSQ M)%WM##N:'*`U#*H=(!D&\6J/$\=EC<-PK8YJQ5I;:4E:]0L'<$S222TYF,22 M8C:#U!\(@_"D1@_"+A28DQT%Z`O*GC-VHS2Z\\94]@YH+_#FXZ]H#L40\MR> M8!M=)"=.BL+4.*!S(DQ1@HC0]IO7\J4WHE#43*[1GMEB!8+3VI2&H6HF9Q63 M*4P+,K##/ZJ$X;_LMXX(Z)S3<&GO3[>TU>QXY-2B11<^W'2^/"R2N4S-Q/Z! M;9F65PZLS=W_;_/+MEUM<:](A01J#O@"?/CWMQ]?T-<:S;7?T]__Z!,`[XB% MS/:G/]JTZ.Y9]:NZ&MLV/_.TF>>%,F?Q<`H<#"0']@.(##.'&OSNB8 MI)Q`88A;A0ZBSZ$X.HINU'T.]SERV'...<$"C5W%#K+/L3A4B(U'+9?GK?HI M:%!@NHC;A6RO:/83OQ"G#A62,D;!!*($Q*6ED+)85@'89#LVL&EO1:.L16Z MZY:MXZ"PC1L,1J&%`=T+URMOHZQ=H=U==]#M!EUO6]8[2E=&L-DCR63=.98N M2OYY?OJ^?'[*F=^-=:=2\]*VYX$+;/, M4JT0^1&'OC_1R[7]YI]+ZOK&P9LK"ENV5&Y7]CX[+[\6O:=:G5+.'2\OV5W< M31@C#S-I@S03%9I`G*#^!^?<_D,6`A"I`_!]TLCNK5D^;_X'F#8YL)SJY MM,E(O(]_I-9$W5U@(NZ.N2JCF@Z45`JCZXVLM9Q"EZH.DP$/ MY$7,R>L:Z\M/HOLL$5>CU0!!!C-[%\S$%&?O"\JK?;6:>L@QJ0=_57RBN(3H M$0%I12X*&[L*I<++MH,M!PLJ.VL+T2T18X@-!8*A2$ND,!]LK_]1XN?@4.)0 MRZ'":7`B?"9QIN5,X:WPY<1[86:_`J>X,$DOXM'^5/HXP+>IA$$VK].>$?X2%`(I]`5Q]KF MPI(>N7:=*!-W1L;*-]\5W\J84]9K<_YMYW2U=Z`]K\@%,U*0RR4`05NT(!QU M0RW@TBFI1T@8:1XX?MC3,/(R#6+O5`E<;F_X.J1[,`W`9U$GL[BEE`]6O@YT M@.Y9D>W0:`RXN:>A:`Z'%S1%'KM`^=_Q;;8^IR-K7 MCBETT/\L["0>ZM^(L,AS0F=14R2WVTXZSI/G;1<=M\C/22U#!IS1FE'-*#EJ MFX"!J"%8X&4];!-+UQB])EJK\%I91-MOQ125/U;N*T_' MG='*[7.5RK20VJB\+L2T]6+F\0_^HE@#]2=FWI10#-JBODA`,6`>]@TS`^Q` M8(UO#?,KVQG?.?*2[QYK(.D!9AD[RAP@508&!#$W9=<8B:,JH%+9"0(JS=[E MU0>#J%^ETJ&M@IOYE`(4',#)L%58!_M5E)68?O#<\.SN2^X[UZ';JY*2Y10? M@2.`/Z*2QD0/CR!V23)B3642*8$`Q9!QR+G6M=KUAT5NL%BM.,1VP2G"/AT,QO,NA]V-^OUM+36O] M)BLX:OW4BEJA;DX$&+].<(N3"+!P$N6;4#9C=Z:_Q&`B!92;1>\0E\0AN"%9 M06Z"T<+8Y>Y\N!J8.1FBK'4SQU8=3P1PK/QOC&F>ZA1"N?ACF_M*4Y6[:`)- M+>QM4GX'?1.HUCS:,9:FGQX^&*.$FMWYT+^`ZJLG=AW8"[9)?4G#0].JYY`P M/&OVO`YH=%J]4^?2YW0J)$R$T2"BR"*><%-`P:K"#LKBHS@#8%3K?5Y,K0Z' M=#!_8?2N$K0VD\?D87F-XC2Z'(G$[\/SO`W/=5^D';'VRA#PB)7J>3QG;PP/AP>Y5X?'PUNC6 MVF]GM\]Y*7P@^N/4H>RA.:^G3F?O8KC;'>T%5H4\X(A16ZO M`Q0<(.X`)DA,T^W^>0HNE]#F>F-:+H:9N%Y3$2L6,R$ORJM]UEU0(`O:%V0& MU6>79T!FL/5(!^OGJ6?Z6PUG7^%?A:TV.!!_ZX.1Z3NPO<;+SH6$\]J(LZ>Z M*%T?$>UCKHJH+(/&].8;SIO3#X%>_#O\6AJ_&<^[K\CV0KXWNN`5&]V!V-CQ<*3#,?*?>B`Z"_)DY0;#U;=,.DI]N3RW7V9B6V3 M&[IW+%I=>=6'NU[O&FZF$E.=JR?__-O.;S``/Q"._I?NLH]MXC[C^/WNSJ_G ME_/+W?DMYWO)W?D[_>C;OB5@]][M'/8+SS=UA;Q\Q);]7B84,OPYIF0)_GV\T?/QKS/*9,]%X=DU!*- M*7$!1S$4C7?_].IZ)9:=PL_"N8:9UF1@`KFHSU`$Q:$$33"H@W8P5MFJA.DP M0\NTHM(J4Z$KS&YZ-S,I3RIOT6\Q']`?,.?H(SXE9XPG<;4!Q'W+:$0E/.:"1)^B`&SR8=@I@TDN^V M7R=5TS3?,5C877>#]ZJK,#2,,T)V=\^9)]3UNJ'QSM.S(V?3);K,6+"4]HJ&TJ4:P%1=TNLNAB8UJS M3S0*9T0V.B4R/A*C8GUVD+4#NXX"RAJ+.BTZ1P!"(%E8^XF%!9-S!@G\:W8?TU:R0KVPEZNE_FJUOU2M:$$VV0L.P9)" MEF2U6BK!U\,1AS]:1BN]:2+_:-$LH][_];#_&>07^G=?#WWF1&E[1*93=%J- MJYPBJ;*24M*:I,E:2DN7I;)<3I73$]*$O#.U,WU8/-3\1NJ-])7P/\*Q$_() M!4V$$HH<"8<(ISV(V%@[X@NR?FN*:\(0ELTX0T08"R0"\"M8XA@+V%9G0DV: M+8<9X7H-&G[RTRD?TS%G%`T%6&*,`&@L+=-A7PO">M7`\/7+MMX+H.%L-!P^ MQ&Q4O=M:.MD!]@.<"19+X*,^J=3[,W#41?MK0DKU\7],"^5:*.=N68<'^A/N M_*,?``NCNN)!:S9K]T1Z3RU][B.P7`[U!YQB%@3R7PQF'#GS)M3[/XEXD5$] M8;6Y``(WP8,:\^_5S/G71&>1]<#_.(9Y[8C7XS0F_4.'$\ZYT6W2[/9=H].P MP`VPRY8JTD/.72+G%=2\ M6BCWETM[^#W"GOR>`N'@'8(C[RC@FENCA]QE>J!KS/>QZV-JWC5/S7<1%;XB M5/*5`DXZXAS*MTKI?$GK!?V%5@%'<"C"0%>S160=T#"++*>)W;V!8%KK[=;2 M4HRPX([@`-<).D>\P0E.!>I(*.2U.:P#I7R.YYR#1DP)1V-)>1B1.`D](X&L MU"KITC'I'FH=PK;^Z89(%LZ>O>0"Y5[Y+WJLN`Z6@PANGNJ4-F!33P M-$P99Z.XNGR4:=8AYPM:_32O!<\:[GSM`=]."9E^<*#0.O[XW.V7S1$;2B9^SYXP/20">_?JBYZ_"/ MEY:&%&LN9U<&P?TGMSP;J",J9U/*X/X3E5WN!K+0.NOA;4\@*G)!GPEPP$V[ M&4S&E#`1HV.,`?DQSS@]SDQX]M)[F1,>`_.GZ=/,!?H"SF\2V(%OP,2M&0?OKE>Q$Q!:) M6(C-?N#7+49>BHV'05@G#.,;B\+#=Z]*+AJCN&Q[#3\"_T#5CQ3RB)D)D39\ MU9Y`JQ%(`]N5/P/LO\B-J[7_@#0M3N[H[=\Z*3*GT%G`UF[?_*1V"\3G/]O\ MVO6["Y^\-CX''I@W3*I5<*-"-[P`?]!?"4;$IA;^:=>FIDWLY?#EZ%5^GEMH M6F#_SGW)/VCR6IN`K4F)=$2&(ULB.RT331/L]RUO$R>:3K`NDHZGR0SF$SUL MIJO9+[)TEZ@6V?1^426<#KL%4WRJD)%#?L)N<5M'8S;:ZAX5B$S:,X8!3#\& MAP6*H3M;&4%)^G4?\"V?A0=5TPI4[YD>^1[4Q,>8"PD:I[%AD:>JS<45.QRD M"V!U3!J+&40-%Z90AC&#XX%>5BA]>PE*M72CU)K6P<%D8O@[I^87WAU=GV@! MP#:X<>GFIN,;WSSSEQ_[G]>^VLNTOJKP[Z- MW9:DH>)2,H=PT&]LO&+ZA2PQ2#,=P4HR&@QS$,;=5HDB;>U0B M8E$/QB5IQDB/28>>,$;'\$PP/3ZH.R8H4_<2E.F%ADXP2M2#X]2:Y/B5X%@L MK-DB,T2A;>@+3PP^]OR3H>1,C7YT8]=Z-7U;/>GDX^._N?'-;P?0 M2.^.+][_^?B[Z#9`)4.%EQYV]11LN6]8-FP&\70X!:C?&;=)@OEI!]2%0X[J M3XEDI^M]\BQYF?R4O$LNDG:+"\3C)(=R#DQ$6&[Y;D2GV?AY,4Q3F"^*1;DP M8<&8H$["Q##B@;>"BSM]$<$I1"'GX:SHCFW"?N&F@`E\]GK5M(]W&Q[*')@U M\T)V5^LF'Y*D[W]T5UN,$]<9GC/C\1F/+SL7VW.Q/9X9K^^768\OK+UV=B`! M[W))LV)#"6BA*G=5::%1G%*U*4E!T#ZT:1#1%JE-:0")1A6MEFXWJ5158;L" MM&V#LJ55!6D5+LI#>*G82)%8TS/V0NA#?#DSYS_GY;]]__>!_X.2+K7Z'*+C M0P4<1VSQR,I#X\.[6K65V_GTQJ'-2Q\68:;1P/,V&)]Z=N?8TXVGO[UK6^>[ MNTM4T:Z#\H.;^,>HKVI8';MI90*7NY-;S%%>%L^EN7A^M_N2 M;RXYEYI+7TO3KZ%`S8"/IFI35F4&N'ZG%=X,@=`,V#RC[6I;(-JQ!I084 MK:9C^DT=Z*_^@OD-\R?F?<;!-(:,>:2<)N[=DIMWF;NRR-B[]KTVVMZ[*\IV MZ1SX'(M0(!GY$QEA%+;\[`U%OH2DCHU'R80!>M((11-94%G%"F"YUJ*@*X;L M$!N@:X4Q4*XIIS=]:6TJ6)S\5KER]L3*USDI`//ER.'-3SVI1,;V[QUXYLR9 M],9FC'=!5F**X#E0/7ZP55^1#(AKAU:OWO;2K[,!OO//O2^OS_7WQY-5TWCF MQ6_^F0UX(!Y2B3M=;O3@-OYSTH4IV$XKZ@Z#0"O`NBV@N;']E,MIA35V5'*K MEE\+M-PS"(T]%M0H;R:"H2/%)A%1X[Y\29Y'W24W_R+*M]K7T786&[Z+'L/S MMG6^&ZRV80>$KU1M@H"<+P5BK+^+U2L$Y[(*9+50JF),K"]?O.CU%U+54+'? MW/R]D>I>XMF:I!?+NU_LG-VR-)F-Y&NF.%Z9")5_@$\N:XX'-QWK4%WUHXYZ MQUJC2V"]=[T/;W@;/MP%*4F"DC0461MY#NZ#)^$Y^"Z<#LX%KP7O!/L8']./ MZS$ZIOC>C:DQI;\:\P\Q,5[QSP"?E1`LE[A*4$6&=I']/LQID(`<#8<%=QS& MXTQ4U&E7IH^QZ6L29-2H#/@K3YY0]$(I4L;P.3`FC_N>'YT M8'SKCK92U"HZ#8[5CP[+A9=/X:1-CN5E7OS@ M)O$/XCS"GN]8-8"Q"2$AXBZ:;G$(]B@(,YPDB1*D@Z@21,#P1%3A5*Z M-E+E+G`X-P,6+5J05'%`O"`2(MI.C:HVU%QK+TW4;BQ-"+6V#3>V9D%=0D(F MRS08B!:[()A_-0#RT)8D?(E_)%N0SR!&%$`2_2JX5EW1YSC)_)#VUE>`:KHL M=:;+G\K%4%C-$.=-W*]16;KS$M@FE?NR`C!-PFC>_SN^W=I?J88=YD-?R9/( MUQ*JX3\`#O"D3.N^&,=Q?$"2=3DFI*5"(I,T:E35-2BOH=;(X]2$:TM^CW2P M<$PZFCE6>"-TCCHG3W/3O!IV)*1>I/+Y7#:7R].94#C6-D4*K M4*+9C);J3UO8JO3(?O80^P%+L"VVU%\IE8VYA5FVUFX:$V*[)E^1#:[6E&^P MB)>+;:-=:]Z016P8B4/!#C="=4@R[>Q$FVE`IO'PI9D5F0:%DH`W8)-!&[+1 M)9"/)0)EP8Z\]H6I05]@WP`?QW).UZ3[B.IF(GGP[UP%TGL]QPE'J0B"\6RP M\Y[Q-]=G9N=JHM_.%2'$/$&A\PTP!K\6"/M(T\0YN2^I=7X"CM(FI<9GM7]_A:G:BJK$TY>TU1=9YV$TRR;*!V:SI9- MU31@N=SB",*I\;Q?/V&<-G`CP^FL;J*;\`1[AL79#`<-J/HARVM$V="=IH?& MO%*8H)60['$[02T5)S`E,51/TKUS9WRH=]T9>ATNCZZ*[M]!W-GA6F`Y."[>#MX7%X*+@(4EO*9A,!M6($O5&(XJ* MJ4!M<:CME$@DP_E\WGS.Z_-%U!PZSU-^7$BD";^2##AQU_B`KPSMXW+YT854 M`$N!5+44J!ASC>NS77%;,YH&^HCV-)\??IB,G@WU$$(K>^TF!K5-ES@R5VQH MMT,?[))HZ.]!]T/8^J+F\0$;RH$V-E@<)OU]9C946@8S'!MH0L\IYONTMS8( MJJE2J//7\8.O;/LJ^,][J^JIO#@&.WL!`>4/-L#OGCK_OL? M_7+'D.,JZAE7YPS^*?DC+(%MMTI0#LKO]!$`4JPL_:RSY*S!IS,GSB*;8/:'!S&/#E^0E>;:W(M\E0[Y\ MN3AP!$QT'4:\I8+JKPG**ZJVIXC4H)I30`38%::B^0Y2)%E,ZZ^(T9_NJ>\" MQH^_CN-X\JF%7QT_=J#SP9XZ2&5R+8%/N&#LA4.G+GYYLNS^[>%#;ZT[_#_6 MJS4TBBN,GCLSN[.;[&-F9]_=F-U5D[AQ,R8F&Y-:7$-43,S&:C1HE5@Q$76M M^*I46YK:BE2E4,'82D-CI-0?(BJE)HV*J$1%$<6B&$2TB)2B?T1!$'/]]A&I M8(B"=YBY9RYG[LPYW\PWW[6I>[OZ#GYOJ>A>V)O)!_K@;V(@K6UQO,PL^^3C M#I'Y?:HLPVZ+VT>%'(K*XB!M!9H=!:+2*5D^"3M)F;S$5U2HW[[Q?VW#*]/2 M@F*55+I-83&*8=#C3@G*9RXJTFS,3B&6C2%]T]8]!_^N+20]JW8SO;6Z;5^^ M]YO0N#*#H7KYX/7!`T;PK*Y0/-,CT:N M]"[L3NGBC]A:R2Q$(,+Q)WX1F0&2?N[V.>@-M-P50ZZ0)@6>WQ3!`>&F M$#!LI]Q8]L=>E7)D#RN).W,F*$R%1Y2L+59FW295:3XOR7WX8G$FZ3QY<2M= MB<4JTU7IZ'1A49Y9!E*\CB[2FW)RG>&'[R/?;O\@O^?#RX'O@S\ES<_+YEW")G,P=*]DUPBQ*B<84:,V%BV M%T0)!J,,T-\8N31@L0(VZNT*H,*A.0&7FUSUIO[4R'LUP:C\8"@\>LS8`A06 MC8L4CX^6Z!-*RR:65R"&RC?=L8KV22,_V/MJ$B[0L83J.8GT!!$A/!$5M-+Z M"#68AIEH0"/FH1DK\`6VX"OL1D=0"_HXI^N"*,)XE!*_BOA3B3\#LXC_,?$_ MQ:K7^?P>'^"W^$U^@U_GU_@5?IE?XA?Y!7Z>]_.3_`3OXW_QWWGWW;%W@Z^, M?_LFCL@PH2T[KT@Q&PJN1%C-8B.A<.H-D=V%D7:E&"VG;1HX)4&C[$)#_-5^C,384F>3QZ(X6 M^^2G3#6ES\^6UJ\SP(5$Q(0\R%TOB0MD3:@8":\L ML!LA`5G>NXP#NR2!$(V))D*%;HR-BA M4$:@%1P=E:GM^"QE;[][@Q2\__SG?S_.?\[=NQ``>J`#"H*U38F6RL?>S@*F M'P?$IMJV5OW7E945]#@%J/GS6N8WR77?-Y'_C%@\_]%%\WY8F!4$,C\"0BT- M]8FZJT]=^AB(GF9,>0,5/?IUVP%X,RGW;VAJ?>+K^[L]2WD(Y<\>;:Y-G/OT MQ-VL-X%R6U/BB9:,7WC^QGB3LOY8HJG^_E4=[P(S.]C/O2W-"UO9)Y^9<=O> M\O/ZEO(_363^;OF`^ZBK%=)5@P)BCK(!O0'K,O$J\?/T&,"VI0];?U7Z,7JO MC3)=.0+%R$<[-C)S.R[B?F3#C\MB%.6].(U+F(!9.(YJO"$>1!(/H0)-8B3Z MBP]1CC!^@R.,6(1F^E;A5_`QZH!UC+IRO($4OH47!1B)*+.LP[#"GJ(PF3V/]"=KH>+W*&K^--PA_Q%T[>*PPY6G;(KY4L):A.=K59RZR= MUA'K`YZ("STY_QK"!+3B":S"L^SW.>S#,9SC67V%Z\(C,D4V>]@K+H@O)&26 M',!L[RO-2E+9J4+=I%YPC7*M3&]+7['F6R]:)ZWON7L)#V?OQP.$H:Q1B90PXG428JQ`@QBGV.%2$Q7M2(26(:SV>FB(J$:!3M M8JEX6FPB;!9;N8^]A/WBH#@I3HNSA"OB2\)WTB4],D<:LE@&90UA)B$A:V6# M7"";Y%K"-KE3[I4I!4?^M M?NO*=)6YIKMFN'/<%>XV]RON/9Y'/&]ZSF,W9_P'[NG6IQ:+Y$OR/U@J'^1[ M]AX@WY?C>!+M8H]XA9-ZE?=V".$C0I`PF-"-L)PS'!B\I[BHOW&W3R_L5Y"? ME]LW)_NN/G?VOB,KLU=/K4?W;MX,C]NE*E*@)&Q4Q76S.&ZJQ<:X<0%;-A)4 M)&Y1Q$V=JJK;?4P][KCIMWL&Z3GO)Y[!+L_@34^1J8_`B$")'C9T\\\A0T^) M69.CY->&C)AN7G7XB0Z_WN$U\CX?`_1P3D-(-T5<#YM5;0W)<#S$=/OYHXQN M@1)>#$ZBNYW8Q-A$>T,.B>T1-G.-4-CL:X0RZRCXW/:DGQ]N%CF4AOIDK)3; MF1I=P'5:U&<&8WDWV?I8;!CS#++SJ$Z>9(P9&F]D:'0R,,%U.I64U'!$Q9'H MY*C9$]AP82*:T*\M4YF"* M6#+9)1D^LS.9S$O:[T&7G!+XJ2)X0Y&"DX!7)24Z(HZIP_#EV0K#9_C85BS$ M4F6\7C\>+U\:_A]R(TU&>R<=3^_P'+0UMSW#7"?@DV148)9[.]KE=LPFEE.W MG+A25D"E[3*QB3B2\JN,Z>>:`8-XGQVO7D:VNA#9Y`<[^;;#1UIDZST%CGXD M[3[B=.KR*>=[UL)+VH<84-:BAKD]I*6D@TG]S.$G7TZ\@S7]LL)*DE?)%[DK MF`L.#B%Z[1CZ>Y4"--#>UXXA%C'W0%*#F,_[-BC8R_O!--%KFJ@\/4!LF2:" MHS5QC2,I):L+NM6N\1Z]WBJ]&3I$KU/Z7"M9._K()7W8))[JC, MX+=\)[F=Y"2V2!MM;AGGMTS:-`/KR*\CWR%=I!G\(C93TTQ-,S7-U*B80RG" M"G.OI<32??_C MO.ICFSC/^/O>^7R7V(Z_OQ*Q`,.$CN'PL2A8"X:-T MZT)*&A:*@NA"LHF.D8U.D'4P#0$K98Y#D*%(G42V#G5(3)O63BTK53,ZJ612 M6XBT-';VW,5M52E_3#O[WN?N^3WW?-WSON]SRE/*DTI4`)?73BI.G03>DXEJ MCJW/X,\GO:RK*L!F\$@Z607D6#KY&ENOQT=1A01#1(.H@A#H8103Z2'L$6D_ M]HCX"VFN`A[K34=>!=*3CDQ#.O8CMP@^D_9.`W=E.MG!UA=@;UYG#8HQ`GTJ M'1D%N#)==9>M5V,G_X%K967=&`IPG[@P#Y,.*#/%:FKW/`>&-['MKQ`%S7E'?Z:1(?E8!S.OL"*CI M=6?PEC1[P"M8D+'[0>,S50EV)[#/\$K6715D-W-OL)NX`^R&14O-,9&LX6Z* MX7S.*^HM;#UG8>LB=]G:&$229D/"XVG6MVB\QBV&5QU9Q[H@/,EUMC)9S=K` M).:?8I_>0W^;?IH.TG[:0SOH&A'FOH:K M%N'61;A5A-N^AMV+\+E%^!S`2^;X_SBZ&_XWN8FVLT?'A`ZITQ[OAK,S]:,^ M:`('NY8O'S]Z-M\Z.3J[=NX5Z([NU%E[=RQUU!Y;/MXVM@0\)L!M]M@X&HLG MMXV/\=VQ=!O?)C96$T,G>N+?L#7RE:V>$TLH.R$HZQ%L#<67@.,"/"38B@NV MXH*M(7Y(M"7$%M^WN:%WB>/Y@P<[>GL[8!+`-Q2B7J$2L.+3J/$:@9LI*4QW M?AF2T,TD*J0DS21)%!=(Z6:,S$S!)]:F5I/+M?YQN"4;7J^:#;>HLF$4#6?# MJL5ZLM\,4S0U0AWS':^3FNKJ8AJ)\/JJ90CI2$BC*X(&TW!3( MX+)K2KG$+[D)JZ<##_`*9YF#)[C-45*L\]?5DZ;%/(Z2N)T MT`&!71#:7\"C$FM5A/M;<=U,L6DJ.V\,WS>&Y[.A/W!UQ5E3,<3Q*#L%P4RI M'JDUQE`?]SM:Y5)-57M0N]9@-!C5#J?#[PL$_5Z]<*NWN[%378KU.EHJ_O1V M/T@XU2@8\/N$"[((0)#LM]2T3;[%[WGK8GSSKG9_J?'2LQ] M7K5R:ZW;:*0F)\D2S4I[:VMM:XD-A\O;CPD=1- M[44VY$:K4#,:XUF94JXLJI(K%'*E7%;N4A35-2D-&IF&IIMES;9E&?P97]AH ML]GE,K3"5BW>NFW!PB*%K,YFSN!/)UA7_2J@O*SNB90:JHF5F?D8U.P/YC,[,/XJ&'S^:AX2&#G-W80QA81#.$,?5T=FP<`\I M-AI87(J]-<%`T(OMN`C;;9!"(;N$W09I1UZD\?L<=ANAUQE@X_36&/*0R'>Z M<1XBGG?J=0YCLJIWAR^T[1W,"?2FRF>GK'G6@]E5`Q&IM.M=*R[8P]1-)K/%Q!T1W6GVJ/1!H)&J#6URJ@QT@XGH>ZX-WA5>SY^R+WI M0?'`CV?(#DR?[[(.'OI+[GQN_G+NW5%K[15L@59%]"<`_JP&?W1H+;^\@,!* M%2V%/RE3TDJI2BV%.C<6Z];(KBK->H/H4\N619\>9[_IDS&$5*)+J!T18OD[ M`\&`6N4DG$:,F5J]/;'AI:ZWVS.HCJS;]M?C5X3_CG;G9OB/?66.Q'OS^ MNW@G9J]C/&K=EL[].W<%?'LG]SZ>1?>0%GQS_%&"28(A"5*J($A&=9J6Z<&S M7TJQU*6=4IAU^BEK?]ZS[.&9`Z:\7_A7_A-]#:2(0>O MI2IE,@589RH)LUQQV]K_ND=ES:T,AQ#?4>DT`:.*Y1S+UD MX1\$![DG480W(9+UZ4?5[B$J8(&_ORM7NIO;.]8FZ/P(=Y50',J#G>'.?;DA'.'0! M'2'/=C$/;.1_NN@'=MT#Z(>_F]9VZ:`_YM4*.4E(&#W%T'(3Q$:0&>R9E,L5 M9J/I%NX''R[@=I1?ZV&1SX<:CD)J6Y[,S.,G+A>\^YYV9-"K=;`86OV09K4P M0:6TO]Q+=.'6[_V7Z3(!;N*ZP_B^?;O2:BVM5K*MW=7J6AVK8RW)MBP+$X'E M"\SAX`R8A$,%2N@D=MS$8'!H.$(=21.&TJC0UM!DB):^E8T3C?3>/ATCZ?>^__?_7O[2ZNE\R#[;#YXV MDO-(P[V9+1'"X=)5SX=[RBN=K.,=K2]TWK\)^\FEB#6/)8"2.?B2?M"YP[5# M>E79&=T=VY$XX'I+>3UZ(/'?J(F,VJ*X0DPB)NHF5DRL;-!-Y:8$FRJF5LZ' M6>(IXDGR.6*%<95II6T%MY+O#@P0/R4W),REA:G(NL]-%NTK M,YD[O"?P#BR\+XRC\$UEBI*E'8[C5,>I.$`I7'\T616_-)+-C2`+U$:L-E>; MLW"C)5-1WK`Z4QF).26VQ$!C@(Y220Q3\"0H=I4F,8O'G`2&6%$2`Q$TE#BM M2BC!4<$Q^6("E,S45W! M1)&YXJM6K3TS]^$MG1W^R2M[%CZ[987Z>?GTOQS9_XW'[U^*_^\4BR MU_O\XLZ^S=6'6C?_$DZ.MG0NVM@]^P?[I]*UB[M?'/[UBI799-.Z=];__-S0 M*^N7U#ZF>0N.3;I_&1Y!^\A@"G8RTWJ=OR[\(Q!3'7&>/V./H$_L<@^Q. M<8?C(/O[\(?A:^RU,!.C!)X70AX((%DD!'CM@@K,6L0`9AK#4_L4DC>1_9@% M6!#K8]&B_I#&.%J&&!<`(S_*65&KSO(YQ!=998&SYI=:_2/:7CFB8TTRPFG0 MF.K-9!(8@TP2H\-4$NA8-(RQW;`!RR*RU2G-+_!1D@F[UH#&[0V]E-(6!9C6 M!-[P,DWH!OI^N+KKE=.WEW>N/]OY.OU$TYH9[>M9W_3'JY2#%W,G\4DS[?2& MT&5`_/;HMJ^AK.[_=)=ZX;F?-05+0[Q8,779-W/L$TJ-_W[C"B@I<#QP_Q;8 M#`^C>N"P9,:!1RB])<(5"9HS1YBB"$DR`B^DV]3*^YEQUP#W@&X2"QW;2=V6[>S@ZZ!SW^1E,C@^O1D0UU?!O`>1X] M!`$0(GQ#QXIFD\B$:`E]@=EC$W`>8AP#G@64P4/I=&56]$8#38>MZ),Z`=IH M`R61#!!LM([@/8#"\#*.'P9M&:,A(QDHZ#$SD/+5&7`:8\!Y#(!F]'<@;L"\ M\1&[D,_SFJ.ED;VF[9K'Y=.6&DT]#R34Q\04$CDNFOG"A:+%%G3GM3F.Y4"< MO:.-Z*%=]+'DVG/I/C:M9]-H8E`>1D4*B@!`WIA"KNT"8SY9)<>!-!8.2P'< MEKNI+ITU:S%X.P34Q*3F_/_F5Y58V_(W6MT1>S,(X@Q>E;^4_T_`\*//8>Y> M3W>*#@0H+FJ>&3G_P3Q[58E1%T";A?;-AX+?NRC/&[$`5HE=SK1N$C>Z\`FP M&2X0'W$=!Q?`)^!3Y4MP0Z%C%"N9Q$#4;Y'$TJC/&0P;6"/EK"`MP6CEC(KV MOY'@(Q*09*`T&D,R,L;\_@`5'@:)C%5X#)^3\3SO.>6!GJIR0]C"#N/P:%4" M%:5V%/AXU/?2;*XVG4.HXMFN_!>6T=!G'F)E$D^CL>`(GOE,B[< M!C`?W@8B?+0-`,G8AGW/];3B+!B>+X)B-RI-\_]G*M_./XZ<:7]@Y^ZV,Z^ST MGQP^M`ZH>-(=T->N@%N[ZG3RGO=>GJ$XO'NWWIX?QV^YTZ^=R/AL%6HEU.HT MHFP<*>K692A1TNN'05W&BQ;X?MFF M-Z-PA%CZH#4F&OQ^MW[)7NX4]Q$'N6%<=TPVSW$/X^11.5`P.#7[!<*GM1`$ M%,&;U#`U;!\2OZ'(:LHJF45_R%\LB5S( M9RW&Z1C/\_E0E)YSR@$<",R0;&+"Q59-9@4TFLS4[`.1L1J<,4F%!"\T MN)QNI\V#AVG6M?E?BWJW5QIINN/69#"4O/*`^NEO]:E':/5'3#H?J]")B$L+"V(>9 MCF7!5<&-0,!'2YPE M#!3\L9`Y1I44ESE=KE"80D(,AZ'`=QMFT-V8W"KC M\C!.#RE6=YB`&DPE,@;S;G9D9"1=$%NM-FG/Y=A5>YI4U9>GWO,_O>9[?*>/7EO[J7(/P7`4/,>Q$ M?ODWPMB'(98]#F-$XF5-KH))1,08A'$*/YG&8S*,)_^Q]6>91XAM58!>[A<24P#ERW-LBIDGFAY^9CD*=2J#9;$/\OQ='&BT M_#POOAX-27Q8DQ\5*BK?5!6JC"*'"#=$(5Z7SF:@6,5MU"HY%$S$LED]=D2^ M(>,9>:'\@4S(IW'RG>;Z01WI5G-3+9B5$(F@I[*?5]4+`0.Q8#NY,21:`&[& MD8S5NE;0T@Y70DFI+@V)5QJ)5Q*)5^/7Q>N;I*MM&D@?[%(XCI!3,B83Z^^Z M&A5'BLW,*>PX/V+<`LD[RII4;ZQ0QIDG0DGCR*^,F]<_&[X$>B4H9M$&X\E# MO3\T;ADGC%'CO+,^*$=!S]99E*I:O`UKC/6Q[:<^!%U`_/AO)N^0MAV&O-.A MLBWKYKOCN$/B;1I"UJ=%Y3X^HD41]?1)ZK$2[]5D3N)%358E/@E7F2-(10^Q M#I*DZYV-,441?5X;C>O)B$BS^T,CVB/PP,CADA[93P]N-;I)VW,0F([R?'P]E+:.J?OX;HB-!_-B2_,: M`B8517+F29E@I&2GQ+OAZB`)TH,J]KAIKQ\6F[),SB!^3*H7-A/ M[-T,:K(<8M)`M;S'BC.+`-)07]\0O@*ME6,@H]@ZME7]7+7.+4^4MW78%%,X M`$Q)F.4DW#/^BZ?.SP_6+PDO%E\2 M]ZFO\J^*)\0SXA7A%NX+8[Q7PA?B*.)T>2_U/L)?ZL])W0D6],DG?"$ M/0DEW!KNYPMARIJP)GWPPI>TO-4"DHE$PAW6^;#`.IV-;CTIX+H`S_!&3R;" M`L\Z:0IC?$&"XOTT+FJ"G0*-NC>38.J"KXRE"NL!5?L+W[W/8_]1;PX.KR&F,G M^'3/RE)E?S$73QJ[NJ!NG5.8KA\1VS;.A?RQSM]@?/=H^9-9"4Z5F%FKC1]7 M*@=Z[+)"^"*N[C0X.=O8OZF3429U_@I\+PXKYSO7AK:$7@H="AT/#8>LT_3B M)GLM%/`33L+O)1UT\)0WS4&&<306;`@N"A)!!)A@4@P!)O!34HX,<``Y'_0[ MI.!F,WW=W":I)H*6!M/.3#?#"^6!0#S0T@UNN;!V]/FI5J_]?2$%HU; M"'SY&>.74YYEO0=K4:`JK[LK04!M=JL0L@>$A+W#WBTL%IX1KMKLC(VQVQO= M/"\P-EO"+8IAD6<(C')0?)T=EH3)`<++^X5P3+'XZ+P@A7U:G>;R:UQ,B]": MHA'P!\*"A8OP7()U(2V)BY'&:MUQ=;)NL\.@0(^-L6/0^+[UHONJ]RI'_-%]VWN;(ZXY1]@1_[4@><=Y MB[WEOQ,D"S2=%NH)/!VP"0)O&5SI`1Z8*]\[;'_=CML'>61>8AB95^FKTOA4 MZ#;-J1GC0HI/=:@N!03M[1CAM\`TZ80[BH4[C(.1DO3"A:FCVX'53;>;?@4F M1?A%4((@E3!W2S-R+#F*NW#H30T!OXNEK!+R*@`4X\PP`,;$VZ&?DK0N7P$S\ M`F9Z/=1<@RV?Y13S!HV9)6*.U!)[0IIIEW-1C%L7$K1EH MY^.N:EK4:[XNAL)V!X;7*4"UAYU%@(?@XA"8(H9Q1'':V5_$>@=WY&VV"/44 M1E,-$F!S;$Y'W,)J@QSL-9C/9X#I7`Z'/E*.JG*5;,368TOVS`FW1]F7GSPX M\<:667,WX`(@@=>X?E=Z)M2SLW*!/-BMAO3*/RRXUGMYXMOVGMW$MF?GV]2K MQ_]PEC!^OCF'`A..%1^.$N.06VU8.\CD59>\@]EIWV??5_?WV*A"]=/+F**" MVQE*V M37$P)!E)MWL(,IVVY5OY&:?!NGP]QK#&QH/W@]SX M_?&,&=JA>K'PP-6F1]C:7.=8"66NJ4UYD_E(K0TIBSOFC!8Q6X(J`DL*+@UN M>)3KE2(64YP..LD404*S,=9&LHA)KD@18##/HC>J/M1D/O/X`RBAS6B%P@)@ M1IO1VM;2/)G98*J%+PG%(`+@UWQ>*WJ]J)62"?"3UN[GAU MO]]Q8@<[<5X$2*D8Y5G($&.C"]4$H2@!*AB;!AE-BZ@86XNZ16@\"E.5#J+A MCG:J*HJJ@:JU:U'%D"9U+.K6Y8]506L'=G;N=7ATVFSYG'N/KBWY]_T]/M_. M[=]=NV[WR4^6)%QP6G.]V6_=N#9JN#8X<+S:J7]/(Z(I.(5P;4TBM`EN0L@' M?0A9EXG&9`L9$`W)H/T]IX@XNQ7H(4E:C7I["@)D-)`N7`\7T""L0;)J(LBH MS6?=9)VT3EFU5GQT`0QR;R`*\&ELJ89PG_[MHR1"8MJ( M-J:?Z&?6",/BL&?8>\YSSFO`,Q-$6KBM&,]:3%L5,`L$1"D2#'`FK5:6[#:` MJ)2;DF4_;S(F>$X9)!&M+NH/*#TA$O[:(%GHG_C59%&%)^`0;,X&)45P*3\Z M2YMM<.$(;1Y=G%CYU[MK,BMVP)MC2[MW-UYO3._N[M^%\.R7R:Z1^LC))T^] M^LTKB#V[FI%EX_J3]<\_&OO3)[M^AP[LZ*)D56]J_C-B%XY%$;Y1_5F&@A9@ M@0Z7'_AAA&['M5VDB[GUA:=-E^V7)(NR5>EJW*+^LM68-,2+D)`1`9F,MDD'4\DDS&:IM+X+I5B\JV% M0@Z*8)2TB=:W7+(HG8V914N$"8JA4;%=+$8*U80D)$"N-C]VD\(O.4.P(;O_RR$Q50N$Q@E3&6RK-Z,-[%B1!F: M4'5TN""@/8S;R7V+AP\HJ,+H@S-"0VB"80T,,A#A,SA?$5(,`R,W-XMM_FX4 M6NY)D188@E"7DB/9&9R!)ZG=Z$[$3.J6'UK)WS M<%Z7[,HZ\^%05(YF2W(Q9]5H/0X/RR*'(`FR;-<*NIR0S>HE3\Z3SX<8CU]# MBM0B3/M`K.0DAU8;4U>J8I?EJ`T_&/\Y-L`^L>;[L/J7 M8V-;T+;U8M1!VS[^6][&),0!.+,R.3#<^",\W+7J&_63:_LW?O!%@0VT^I8U M0A*U^!7X'%SZ\;!6EC64,>$..X3&=2A4)*WU9/F%C=(J/36(]?X'UC(`H.%]=&B-+9+_0']`><1Z1$$F0%)6P M<3Q'$D34%@H%0_B$TX6#_$"0#_G"T&+7A,6H%2"?6_20'&4C>2(4C$3COT4T ML,&OJM1`U!/AH]Y(\$WX%1@`$3P[8NFYT3E^MCY;&JWS,\N5B8[G.5Y`5UW1 M1K5O)6S?1J_PBAPJCFL?4CEV;Y"5%PI%">;#$#\Z7Z`J!]JV9(F!A7A@VYBT MNP^^W9E];%/C@^6'ZDAMS$SM6H)I2&T+<&/8W2O!]CTPE3$KP-"V%HXU< M8V1L$2%)9.\A^&UX^-HS6J40-&!P_I^:PYIIS.A5T(UK8>O?Y;LR(L*+]<@0 M/$&?*)VCSS&O&M^D?D]=2U_+W*)N96YF_T'-9LQKR40VQKE]#A_(F\W0O#27 M:BME$V8:Z!VD(R\1JQ2PGZO?QL1:GL&!JY=OXP&%)Q1^*^%3\76(G[VN!%5I6BH7 M+>KL"D8,'"209)3ULDV&)OS7B$ZM%[`AS@N&$XHC$`&4)@,NNZ2"^P MAAW>!W@$542Z;P04T!V"(T/W$UM!I5![FZ3H$VQ1&QN+9R'F(A6<,"0UIV5; MNR(=/@XWMP)$@\\,'BV',SU[&N#%C=#N:'DZGTK1$NM)9EX[^TZ_1!JCG%?R M2\6.OHKFL;8-*]?LA_M03$ZM']D0=R\K/;VY_-3JK9%>04P;2F31:5P46OSR M_OX?-;9W.,,FL37LDM=5>OQM>X;0;--;$/.SFK=TNP"/Z>*%:NR.`>H-\(01 M!DEXDUT!W/!H4"\1P8"H9QD-"'0RA+C%RGC[3#6$JG18"NO3CK=9R-;@?--W M8C;"BLP"50"#^[,WH-W5`EXM]]@\1N\,G1;\.(S!F3H,8LXP53KL!!. M.T[F/(X5;B:8-ED'4$*$62((FC#:=!#$SM\02&C=N/O8'QI?W-I^P]\!J>=: MGQ_?_\+`C[5?M@A5O;X^F8D/?GGUH\:'ZQ+:0$?V[N;DA\>/U]?V-E`S!FD< M@T'-%&@!07"NNG2".T5>L=ZPWN`_MMD M(B3'$[2%XQ''VPG:J#/FL=C'L`/M=C-!U!/T\3A$%R5+GT_)5BFD9.M_F*[^ M("?J.[K?WTD1L?+P9*9\=A&Q<2VB0C]`JH13.U0S;*N17,W@:@++N9ILRB!I`=WU MN[@L=!)$"\=GMSU_["=W#\:+;*&R\X6?7P;Z/\>PU_;,YPMR7.YT,N__\NG+ MLZ0EU`.S]UW[^!QHU[!)0FPF=:-P7Q:12]5-SX1_%?YK^&SLG[$K,3VR*?Y0 M?'_\N?C1Z*OQMZ*_CW\0G8C_*?]I]%+\;WDK%IT7006CY2*^T,Q:QB@?YUKH M97WC?"HI)W`7'I!2"<&%Z3)%G.Z@0";=82AV2Q)O">`)6JJZ``RCR!NEW*R# M[:!=@;#4I=`+8CA\I5Y"E((ZS3!704TEK@)"JBQK7C2R=1;"L*,\BV56$;`@V)4CEEZ%1,#>)H@"$6*`!G2HP!%N3Z+TZ+?_[PA'QD8.?)Q_GX.X-W_P&6XD=0>RP]7B13ZK#&XP;B?OH>YD'#3N-NXC=U"/T;L=N M9LIZS=:RQ'B7<80Z@[]/7\"_-GUI,Y:-)K/+C9G,J,F,Z6%QQ``V!].S[!JO MW3"N?TF/ZGM:+%XW#$E>\IP9F!7V^K%+I`*]WZ>Q=Y@NP":J\7>RN5_KTPJ' M1Y/$[=8V1,?`D..@U8W:AKA]H-6MLV(BXJ18^#^`)]RF5[\"_`S3^U25OL)L MW@<4W&%8:R*NF!RO$#V'KKY0?\S\[MX-8V4A\L7+;W_PW:E72YP5'+:T);=W M8$?^^-MO+FQ>1SSR=\">/`N"`^NRB]8FEP_`#!>&!D9"+HO(_=5D&8$S<;#&VM'CT8775J^7PYXV[V450S,:[/=N%[>4_\WJ^N[ M#]U;.[CIH]E=?$:(>1COW'#/9*W^\-:*B86:Q9%LHQ=[#^XS.]*/+$66(1]6 M5PWT]M?V]_ZP=J1-IPOKNQDO#\6]>!.,="&BO/( MGI0)WF.1I:9!V%#0I>E^?V1!Y%0$B\Q9D%[FX5H-:'?!NFR9Z)PW."8>$E%1 M,6AB2)?.`\0=&'7@H)DMK[JJ\ MZ0*,X'1I\$H!S9,YY1[7/+@"NX1RS:DY==JCT]C9=W8=_O#VS%.A10'G:C>1 MD*5U;QT9^/4@L\1.'*/-U#N'6GN\=\Z.YP&XX^G&"Z__XG1Z;B\1=X7[MEX- ME59M71VRCZXT-OY3W7Y[#38*@*'`JJM4LZCT[,B.\WW88+N_F-EVRK3:S]G, MWL1S!]]^;"#8-ZN+H"E_.#2TUN&3[[_SN^%D_Z[WT+F0KS3DZ[^@-\O(&U5G MGQ-<=P&3R^-"/48RX9=1H<+Z3X`;U:Z`PE^9"WHJK(\3HA4VP0G3:SDG&2<:&2-V,04[`MA`4$JT>9<6F2"F:P#'EZZ224.>J@9?4%0LKPZT5 M^[V)*ZD'?@95ZF1(=+I%9Q`F?'?()?F`&HZ:6U6E>W.I=H,*<&EFKB:@6W&U M:>3J`WI1VINW,"VQ/:TC:"6Y_*Z7NKCDO,:"9:F>%3\8SRQIS&$M79NQT_E. M#`VVA(P^0_W9_D#IB?X=C;LW5LTL2Q0W@P.K'MA"->Q;\@2K>1C4/6J%.%I@ MQAFNB@)AJQ!LB`L*'.?FR(4NUCW.9--MC"IZ&M]K!'-K6IX=-GNLOKV!F7NW`$^ZVF-X%:_M>`E#,9Z M:EO1J,UT\T>-*CBNSA1']E7%F)'EF(5M+#O.$RV6!"/P\498&88W6->$K5&' M,H@,9WI=""8-)<5%W=,X='M2R2[9SAJ16@`'`K"'\QC<)':\2*LP4`3\+: MX5[B7]-1PF,+O[QM>SP(P>B.*C^Z_M^'!V+K0T^AX[-ZS`8_:Q8H1F^<6GML MU6]**3X-M8)#K=S4;47RR/GJZ.S@FZC_#/&S`<"!=H1$!B'$*@&%M-\TL$D949V)).R$.!A8A=]FH1LB`\"JT>R M$4QD\SG)S"3A>\PKR*B4\HY(CTJG)4PJYA0M6AS)1)ZS7#P-S4$15+&@9):O MOH+=A+PP?$:-*B[8\!)N1"M\2O.[,CE%:4_A54K=LHW,#"9! MG*F0T@#5`F@%-N""`H2"RFD/@=(PX#T^4I8[["RU8GU_S*#'`.-C.HK@Q2U/ M_*'KY)-C@XV:0+%F4^,O:=]`@V<-J<78MW-$%&7=;6Z;SC3UYI4VCG`1&,L: MYA[/7CZQT^!A44!8+78"/--XL@_:LP]B'U+U]1#B0FZK<@R"U1#6Q06='$U< MQ(L6EABC*1S#X8]=3G.KPD&*3F"XHBBWQD%%3A"`^3.EE)LIGVPN-2V>]N%> MBZ-LY5L??]>`E58V_D]WU<8V<=[Q>^[%9Y_?SCX[/I\O]IWM\]GQ6^SS2^S8 MR1$[3@))".4E"F`0@[ZP@DHFEHU-;)6VE:X?!F,J+51:0=IH5[15=&N!?9BB M-2I,RBJ0REX0ZS8-MDY=U`^C?!B-V7-G)PRV?7G\W%F6_/R>W__WPO.FTD;L MVI"WQV`0PQ6+Z]Z&:86$4P(0$4$,.>QU9!+YE\H7O#D!=0BOV=#UL?45E.ZG M)P*3V&`Q6>-COP#W8/A78=OCD0J\Q?$@7D;X22$<+O-1(503Z&CR(AA1K0VU4$RO.:I>5=%1%;ZYT,`9>2Q-Z*BL3^L:/'=G MKLE">%8W?]45N:)%C`E:&U?GJC`[5V:VW4D=*=!L9GJU,/7H%$+N=`/M`Q+D M?ZEQN[.2C[Y:>2-.YIE%B;PHD0:ZU3MB-;AQN1->O"`]]8 M>[JU:T0Q>L)VU06,,B'0VH*3%09&0!GE1"&ID5(0P7^8%(02[ M3U:[PC8K[:FDQ#,X1BI.>VS`(]M))2L*5([,1:1T#O?Q\.8N%)QR*HUAN#;, MA;SFCK1NC\[2<@6&%MTB[T#A=*PX@08_T<3;YBA'62[*1F#@Y61O[($Y-F);<]-;JKW[2O76YO'RNJ6_FJPH`ZW MUH&;O"F_';*8@Y,@9$0\7<\N7W`/[9E?G673!3WG/FZ(%#IXY+Z$N`:7WVN\NM&X"[#KZ?V_;' MMUJ+[[_V8Y"M:!PRZ1GY/&*!+%I09PJF@GC">U)Z0_JA?$O^5#92$B&OE;"S M83`L)4WY-._5";2:=E=GN=U@PU&, MQ*)$!)!AN.`R&D$,DC$".@56:Z^SS7`[$[?#%'C8,%;)U:4#"'-SAU"[GFSL M._GJWK5?:?URAR(I9L:YDU@@B*'LUITO7/[D[;Z86AAZIN4X6/OM_,5WMB5: MIN5SAOH8-C\>A^TU`.HFPY$AH>_CQ2NMG]O,H7;FRD!\/X(=A(;I M]9JZF8IS\6(<>S'QH]2EU&+J]^A'J;L)DB7I@1ZS*-@,LI3F5!_PZ>'56G\U"9(:[?3PJM%. MP_:_@'4H8*51='"-QM,DXX1`VN/6"&).P\7D,/@!X[(EZ`AB25$0<8;R:RP$ M>CV-KP3;<.$_YE?K#DZHIA!H/W!WG%>?7D,G["`*BFP(];K8Y.'O'/GVU[;E M0B//F*!Z,MT;6_S,=$/9M/?P50!^_33-<-$B.+L^,?7Q2^=O8'7&$AW"`8Z; M[ZEY3C;R(BCO`8>'_9F__>E]D-8\S@3!/@]QCB'/J^,+?E`,@D`,:*H7@_95 MT^S++."#,,<+W;3L(:%9/;)S'U2ZJB9J3(1%?HB:EFBQ&-F2GP[N[-!"ZZ>DP, M2]$_F-E33<7Z&K.55G5+#17;7'OJ_A+Z*SC+&20+,%5D$`9TH3%KR?J49:_U MD/F0Y7D+%3/V\IEK4/[@;RZ"[_X4[J$3BZH]V,/RWFNJCQ>Y`#R]]AU\=&O? MQ46G%:&,\!];*9P(*%DG22@]YJR=`Y]P]SF4:QC79)%>&`(^A$R2O@1D0[X`=(1`\U<&*7+ MTU&#-$@!+6QGM>>BPH0B'J!C4,]DY(Z]-RV`\>BE+GU]UV% M/5O*VT='#IZ:.Q%U6+!+D)M>>"_]^!D8K:;5'I,#^(*H"RWY@P;5+%(CY(#= MK%*B.:SZ122(IET^5G4D7+"6+M[DKG`WJPLLO;RP"+?T;^""#"[/?<"Q5[C! MQ>4*1`XF8T@V=PASZ6D@;T*0M[PCI1X8LU(F'FA91*]L(YX-<5^Y@8:[' MLY\@3.QP==9*8*=&E^?'Y>&@U.5OE/>6'D=W8`:",KM*(R_CUKL:MYSWE[#K MT!?C2`)Y79U<1ZX+;"6W!O:3^P.'R%?(5P*F@#5@0[N-5)FW":%(F8\+(1=L ME0SO.N;EO9%NFC(1<1MB@#XY()H3)"]3:7LB(=%V&@K8VRD$I*6(Y@NII!8O M8-Z[JYTO36LBIFE8I0)EJ_20)3B#813'(G@0YN]0&`U!%K0E"KH![`MZ_-<+ MF$-O"/JTV0`,$L%(%>BJI`$%Y4O.2Z#*2+OK:Z1(92NH9=;_F_=JBXWC*L/G MS,S.;6^SLSL[>YG9RZQWU^N=O=KKV5UOVHUKU:Y+TC1NL0,U)4!QBDA:)^"T MB`>K0CBJJJKJ0Y*^5!C1/M"7JDI-*E4E`M>@!*$(1`B5"RJ*($`%4B4N5;T[ M_&/'`02,XA_]"O]A9 MG\E]HA`VJ9$#94>RTYX9IS6O-R`8`KMY?[9UQ[[G*.Y0U,=I+N*3TL#957H3 MI=!+[<]DG5G%@&K/,<+0D.&!R]\AD1ID6\1?<0Y(K/C6H"$)%@9N MP(FK47)L]D@A.16'R8*"7"I#>O#%B;S@O'K!K::#&:Q5\KGN;WA1$#U\]Z?I ML7"9WHRS`4/2M/B"40T;..!W8"`A9"I)+QJ(LVF+8:BU2 M+C?D0CFJ1;5:)*"`I#P/>2Q![()*23ML]J[#P`M.(E'N.D/0D&KB1T8P"E?UV40&9Z9*.ZM`,"'S76EW>:VSVL=K>\M]=(V<%*U_([S%2=O;>6F;(ZQO M0W(+"2Y!P/\J6;$?5P#H'A\*D,G2_08<65\7A1RP46R!6:^+OMAJNIU;K[FT MHMD-)_3N)89E7=1ONQ]2G,-%=7]1293PR6(E%TJ?O$#E`X'Q(MZDG^(B6:40 MZZ;Q:]JGU72$U75'9G;O3P+/,E2I\W,'!^U[3^8Y$#&/Y M0HH9Z`BA#OB&=DV959K)FI6HBSXHU5N5%L194E!P+G\:J.64T9Z6@AGO2JHE6 M2FG(8JXAU\#L+/L2N\5>8QFU)*=8N*V49=5R*5416;[:Q%Z9;FJ2;XI&K%ZJ MTA%-*U?HJ&BQHL),^7SW3!';*1\;K9`0:E^E5=K9W5DF.I762CWUT)UJ:T]M M]6O242QRCKR47X86&J)=3SYIF^<`@']<7OA:YCQ]3L/^F'^I>-?]Q?E@1*8UC2EE_]Y]_&"1TC2*"LG^ M_0DK^EGCHT),]+LX37,:=^`%G%I,*W;IJ^`CR]!K/KM]HE/A3$GJJ'1 ML9PY+\Q$Y\U/1H^99\0SYGGS#?.7IF?.Q-F\:.9A]SN=#3D$X:D@+,BFF3<% M9R@,8WPI35M::``N*G. M]IW_N7&(GP*VAWO%GU18D@#]:[N4\,<=UO"XEPGO9->D-?QR-504W7]\DW:/ M:''LS^6\W;3K8B1$ M4?&XHYC;>^OZ#^K[1LY*O\7/0' M_><#F<#[RC-!%+RAGE$_"'TM7`]_(_)X-!)]7IO6_J8_$9N)O1QOQZ\F+B3/ M&W74C_QPKPU`_@H(1^!FT6T+>8FB$6(<"+&(XTD,38KH=/6!V^.5?+(_`%M9 M#:$P3!O5=!2+)P83)(W42#J3'8!;0"%&6$:`G!&NLCRGD00<'F`:+AP:8`;P^P"S@[^P_='#FONG\ M`X\>?^14X?!CQX^>^&]Z@(-#,/\,\#`-4=\#Z%%T'#V"3J'#4*^@KZ(OHZ/H MY"VM"F#W&."CZ-8S_:\V?7:::!6^\2PB#$AP51#B;K+?ASX\U.-LY,KW'O:V M_HI]?._YAY5[OS1L[:>[;>XKCJOP*`SM_RG``-C7P^\-#65N9'-TF2[";8@(9' M["[RV,W+$(@$S:0\"I,1*';!C+8B5EJMM$,1B=Q06C>C=%)E2D'Q@8[C,"HX M1LL`\36(6LG>?G<34G`Z#G\XO2=GS_D]SN]\O^]WSMT-!(!DM$*!M[HQW#3Q MC/Y+(._G@%A9W=*LOY6P]N_T>`70BNN:[FX\OOJ6=4""D[WY[I5KZRH.!]8` M-P6`U,OUM>&:\VM/[P;&A;AF'\ADF7N-]"RF,;PVN:$L.)+W"]E[)^3[BQ=L>.SS\#/(G$4]BTZKYFZR(M M<)^U[4WWUC;YOOAH">-1ZZC2FHFR".E:)88IC4@'K%/L]+4^CRVR8EH!/+%] MU@=*)E?_OK_W/2[LPR-X$6NP@?/[$<58Y**4K.S%7`31+;P8#XE=V$J_2TA# M&5:(,]SC&=3C5?IEPX^=2*6^!BUQ&V]9 M)YF7`S?$,4ZGYSSNU"&2Q"CA%5N0@!0XB6<\*KC3G5QQ2"3*,NM>KAJ&`G@Q M"[,1(.[UV(['B>PEG!)+9;/2;OFLP]9K=JVX/HM3^DKH2$+H[EF!LH9=PGN1AOC1IGQ.SC%UHV/1;*8)F:) M"K%%/":.BC>E7_$H6Y6#JE,;;7V-3#)S,[/))>I"3"/NQ5B&,'=^$']$.S&> MPR61)L:(`N$33\DL>8NLDZOD$?FIJJC;U&[K7!R)9"4<9'(2D<_$'+9*\O8S M1(CH(?R:M7N4R/:B"R^S,J?1@V]P66C"(1+%6)'/Z+<1WSOB?9DB4Z4AB^5I M)4^9J:Q2WU"[-7^L+?:%%;""UFKK>6;_/O>R,[=YN@M+B;B&N;>PVAM9.[MM M8GL`3V(/GN8).X"_<>=_?@=K8*GK0EJ$(UZK""M5E#-G>2SUW, M\&GL9YV>XUDZSNS>8-7?P\?,["M\BU[$!(1*GD?R/.>*B)A9OF4."`ZQ$OBG+@H+K&\FDR60Z4NW:Q,F:QD M"_,<-,KUT;Q,F)Y@.PS'?<;_C`<=.1SN>P#_P&]ZTJY_#&([K?7;A M67E"^G$&Y\G`)EG$NS-!/(L*=1&.\.V3*?\M'Q7'>;+*42T.()7O.JF5(XL] M3=G)>PWK0_8>]G.Q8KX':8L=MMY61C%Z@_6VULH:1GCC;^2-.(&S:I*XG>^/ M94H!SV\-WRSCX[/\[CSW-.]ACC1RY]]*BLS(STD6DC4H?? M-.S&HWS]`YX"J<^'=,];MUOZ.8)GZ%'Q:)Y`R)S^?&YVI.7!A,P>7B"MV?5N_331'2_69I2WW$'_(Q7N>,]D_.W^!QHW-H MZHSV079D$R7A#?5I'&P/OYEN^/SF2,,7MRG9_G"-63$OX/=EN%Q!C]L4)=5& ME0FCV!R2U[\\'METE)@))0RM+[<3P#:]P]T5V1YUHBJ4EUQCU(07!TPE'+2W M&)IGCC!\YHAUW6G_%:_,_-O[C1_1:,KLTG!MI)34;)O=)X9L*;R=4OD"G3'E MEF#`%%L86+?AVM#[DJ@U_+8FU*";24:Q41]I")'S](B)^6M=!]/3O9T6O]S\ M>F1AP'"9MV88P;`OL^,F1.:O_?-(KS[R6HO'W9FV<9J+E'5Z9GEFV>,T5]K& MOO%?F_KT)[L&Q?V.G.%8/G^`-6$#,6YC%J9>K1-`P&`J1?9';1$BU45TXQ,4 M)&&YF502BCBGVIQJV4Y#CWP)EM'HN7"M)MRO2M3RS(1VLRX8I+'W6)F&$U.WL0PL#QD\C8=@_P0;;B;F#/P-<:8. M\]=/-47J]YAKX_8H)KK+HTBJ"'0(T1:,"FM+%+ZL3B1!6;:4YA_;QWVYC_E3 M*'!3D>OB;));+R7OI60[J$?TR&TU$;U4K^>!5K/C(PVUD6`^4U\06,[/A0&7 MZ0UF#$QK@\&IC#/9CJ/&XT2"C-#0'Z$A'H$!>NE4Z"YGD7,J`O,"9JLOP_3Z M@BPJ[T<7:>WB.0@&Z54T@)3CAN5I_9BG$'-1+B=3^Z(L8`R&"$8B?1)/85ZV%XUG4Q7/R_&2XAYF*;8=__CV'_50S;)SP! M,?L?D0]Z=_?N3DQ/A,R^YOMQF/JAU2/M'R;[L$\[:O6H_+93@='L8Y4',8WC M*(Y>.27VFG84(RAGLT]F]RA9*&!WR2F82[F2%[:3YSP[\0<.SGTF<>S8(5_^(FX2O]AQ0D+3>9!1`DM+ M02MIRPI-M?#1P&A+`DU89ZU=)W7--JFCZF#I@F'H1=#"MFR--$(WJ>O^V1BJ M4JFKYDV:H)H&"3OOVA5LVOZH-%OG_,Z]YW?/O>_<^^Z[MY6JY&4E")CELP*9 M[IWI)3,C,U-D>F1ZBLS0F3B9IM-Q,B//9,BT/)TA*LF>C8>I3253N1Y:H9)) M@'*5O`!@5&Q7>'Q5\.B^_@8;@@B=C-M%ZIZ!<7^\79?G&R7VSK%UOZ MQ4"_%NKO<)$0\1+3'J:K%$>?^&F?^+L^\;=]XDR?N+-/#/>)WCY1Q;]7+./B M'\?%'XV+M>-B];CH'H?:M\Z5;2A#Q@MP+MH``7Z3R]33B_@72(:GI/AG.?D" M[5R%+Z,XIY7?*>(<+!(-SZ,4]@+^!`TP/(U\!JU^>RX3H2I^*)=I!_AR+K,5 M8&LN\Q#`8"ZS`[IX$&58DX&?2DXK)?2:;XE>R;Q$?YU1"53_?`"J<_22#YJ?LNW2`]K74+T0Q#@H'^1/IEB?7^U M`+O\T!J\C_J7Z`[Z+-WH8^V_(#/O_0.L[][X(NWQL_C=,`1\GJ;E19KTLXX5 MRAR)0BE6"!LME$*416N>8I6-A2=9"X]8/\#&'H1A>I4R6D-'J">UBWZ)&JDQ M>P$_#U>P+#ZLM`K9[PO9(T+V:2'[A)!]7,AN%K+KA>PZ(=L@9-<(V2JAPF`U M2`:SH=1@,A@,O($S$'@O*M0[UQ4X^&)4P4L:\)RF.69+1-/:O@-;%,$&@OHZ MG602&MGM=9S9)*,G9,*YA@Y6*P\ M2":*U@397[3VDU%FP4M\5NL3,->'D/;AF<7?F.6/PU%D%K]8.0L'G1<'G7;[ M:,*9L'986KN[_HO:7M3!NS_GYVX0O/>'-V0.7()E^E=(/<67F#YS7J!7!?IC M@3$V;`)"EA&RC)#5"-FK0K9(<+IG7X']?_:4>W"V13/NN`G2M:Q!H6QD-=NT$T%!<`Z#A4XAJ-!C,*4;;6:#) MI$.C930`&MF'9$:3R3Y&6])H9T;BZ:XS\3BC<&^C$489X=Z^AS+U[Y0I1IDJ M4BH9Q><#2LJG43G8:T!T/W+;2C1 M)BU#$51S4[7%8_&!E/-1]59@&^OKMSCA+#1;(;$?($JH"B>96S\44`#]0'ED0CY1>Z%6 M5R/75O>(/?(6YY95C^%AY_"J,;Q?/R&6!KH#-HL[X+:O=KOM-I.1XR6_T622 MK3:;G?=75;F)Y*^K"QATF;W>ZU[BK;<%_7:IS$9MQ&8+FNJ#C5?8?`P%VX+2 M92Q],)37\I37Y)BY(7A(F@]:K(Y6)Y+R6+I5C`Q<=6!'6 M5P8J;Y6(7=N(Y:5K#Z?6)O,KMU>V+W_8B?=>^M4ES+L\MVU5J\UPR.0KJA[6 M3=;=9V_Q$4_XBVT;Q[Z[]^(R M&DYQ(8-,0A=TC4E[I%>A15X2H5SRL#E4K520_M;0DTNUNX0%U([W)( M?G]E'769*^M<@8!LY3B]U%[VGJ-'K.LIJ\25O94M(@FU&!3II`<.1>8]YF^: M=>8(%_;K)8X+FR+A8D:+"7U_:/1]5_M?7$Y(:\+:.MHXY,Q+^>6E8G+GY['% MVHI`(,VMK9HX/TMRNROO="'IYM"->W(/`5WM>0@GS0_!)#PU%&$I!U7(NPK9]SB#]D@-\:PL]0_3.GW57=5-(1&ET59DP<>FN;8GAQ`%NM&ZT M<5_7"]RQM1-=;Z9*2T/F<&G$%7*%79'*KKKDNN2`_*C\1M4;\EQ(#:N1A=!" M>"%27N*)Q61K*6 M%Q_O[):[_2XI*8_(1)9[3#W=_[G8\Q9M1MI=5R#/B?R-_.@?P'8YP9POSH\V M.PZDO0%8WV(Z3LYU@$N<%PDL7(%K$^V`E!$JZ0NEH"P0ZU/*V M=DTG=:P;*J-3-:9N2CC M@G>TGML8S]J9'9L_O':[M!_QWJ?H&7P+Y(4DZ/NRMQ!>&%X5_I;OB?!N[PO\ M+M\1[DW?.$<1OIBOX$/#)B^Y'G2&:CDFJCUD46_R!B0CI+>*(7`UF9R,UPOI MH4#>2DA"+26F:KP1$5,JC]<;(:.1!Y(84.9^\;9BE[=;*R/^*OR?WP[\%_X< M'("?#L`#<-E-ZF$AUJ+,6;%4`@6\E[Q5F:?@2V"),O-H:?3P(A6N90E7HK8H M$VLMN!J96-2Z;M.Z'9?.?[QJX4("GAC[3E_+Z_N>D>+8VV:/1FLE$`3UX%4D MS%95::J_V+$"OP,NLRVF%K554!$)D9!#9 MANQ%<,3'AZ\`OYWZ:-B6`032(Q>!-Y229`K\>GJJY!Q3`ZQ-&014"I(22*5? MBMQGS/(H4W>_V>3C)9<_=.CVX&#WO@SAF)7=N&?GX?%?7D!'UT7#T7JWK5G- M6&?VGQG>UM]>9>YOF'?TX%_?.U%B@KOW*1;'1X!F\S`L_ZQ(M0=GU;]`304O MAVZB!$F9PZ?BOUM_07J>FT)QBJ&6).BW9/39$SN-4(X^3R M8C(4=&%@64E,9<"8)I=3"+G!1V@[T]3D9-QN)P>IA3PA)B0DW]P@4=I4J[M- M=-+KW;#;W4ZVMWU9W@IF_P)>^Y`TV&!1(&.2BIY+HOY_[N@S%9$/Q,OZCI;5 M#@'C+`>;XJS`="T$50D]\"UP4I51+`O]_D+.->5?VOZTF/G>B]^&;[JJJ0TX MZK`;'.SPI!HY^3R&VTE'S!FWZ/C4JCZ[V:_1=+VS]K'G)B>.'UU\XT^_R,]A)P8@@+CU/4M.-,U[:3MGIB#-K-B62*S1LBVE)_(F#3S][ M^<;U1[WV"%@&G-9`?VB;/70MMAA#PB$:+<:5QQ#AJW,V_8CR%7<2N8Y]A M&AR#9;^+)-VT6T`)V>@R%>B\E?)K4S6%.N7HC$"J6I6L&E2=5?U=I5(%ZDKH M*GS:6``N.WT2@#MRQ9:99&VMBJV&2[>`W&&@8::B5DS_Z,@JX'KOQY7RDB?? M/]^S9.;M=Y-::U+^\Y?N$;OM#0K+ZB&%&ZPE9P07`DB(7J&'UUM9,!S0A!](TU->88)33"3-W*D!C2JWC!K,:04D"P-V9IC\J-4&`GU(W2V-0 MW@I^N!+V],D*7!7%@EA6X"(BA`2$^\5E@L".ZPR<(L2#MM[XSKCF>ZA@]WK<`^:`HXC(U:4GUHX$I^ M^LF9+V9.]#1PT9"+X0FU9N>L+>BB_,WU;_5(BJ=9[MW"#Z&[H3ZX47XWW=O9 MW)GI[=T4VM0\&B+P%B+OKQ'FQNE85ZP[/O=TYQ\[KW=2/3V]K=W=V<[U^=5B MAZ>SV)6/XCZ>UJNJ4L9N,BCVV*P&%9[*]71G57C40%MEJ\O68:/GZVG:R?"\ M+QJ).!E)PO.YG)/)9KN#"3*5Z.OK(HE<-B)*I#'/4?P\T4=OXV&:;^/G\_OY M8SS.\_-(G)XO+9>>DXY*OY#^+%V3"*F;SK;L90,@8"KJ5Z[#)1M0]A%H;E;: M/ZBTH-3B]0$=V`6XLN4;';BI)'VI"]A8@^(0R7(O*WM$I0*7+6*4UFT]5=5< M6:5%61?Q((]0E6++(*>`)2@^4':$A\X!2H#GX4EY58XE3RGE&NIV-K@"0W/V M#85[J@]@NFK&;C):TTYR]OY"K=F-XWM1U%J=/Y9K;LR^=@)!36SK>#H5JXV- M_0[%XMTK/J[:-+1LUVITM]G5Y7YJYT_Z#\D%\X+IJUH[8S)RLUG=RJ=H6T;O M-B$-&KJ*M?U^]9J7_HE,J`UJUO[AXOZ#BXX@$Y21$FC434O$S+(?K=M?[MK\ MO5OH!<")#!OD-W&!:Q4%/I4TQOUK,J\*1X1QX8SP?OJ2<#YY,:W',EB+4!-O MCF4*K?W4PLR3W"ASP$11<76"A`&572 M:TCJ15EPB1UBCHM(DI/A'%RK@9%E)P.>(YDPZPE9A$AO/DBU.98[MCM0AY=K MXY9RVSF,*^0<',UQ.1*FH=SL;'ADBE7*.`2@V!H&?PE/T?C(Y,#D`%M&`X#Q M`(I37Z&AE,M?VC\("-LD/04]+(X-C:"$0P.11\)!J7WF\BZE,AYHQ?8>NMXC M4!`E*OB?F@E7@\:BRR9J?ZY"=FSNV[LA6)LAJY['2!UM:^MV]#7T%=VM./8, M25@0X1!!OWTUC<9>:*1Y`(DJBB_8Z`E+Z,"&'% ML)*(?:M],GV33N,U/JV)-X,GKVP9.C'[>8_^/J;O_O: MG@]^=:J_==NUB^>QUUY]\,+RA>]\\[VSO]#Y+85F^V7TWV60`A>T02&@1@H1 MG(HTM12M!7[4.FH;Y>^W[E-F(G/*7.21Y#.N%YPON98\B]*?B+\13I:`SA2. M"P0E>'G5)O"*C:.L"H<[PPD\=1IV:S:"T"F"HLAP7)-IXC3D-'^0I!)YK]G& M<;&BKY5*(]/'4Y"BTFRZ]5_,A>[X5GI$V+2"2DU+:,*Z2K7Z%!Z[D_XD*P7\8]3?+"VBL0BXO#:\)$G_"] MR=(79_L.__S<.W,#S8\?/=2??'3A"/YHS-T]^O?MI)E4+70L9`YKV."3VO3^ M^=]>NS:E7?GUTMWEZ[]_V>CW+`"X@C^&$'Y:&_QI`@[9($&2-.63)"PQ)?]9 M595$?XML"V`FMTH&G(@U9:#93#G&-35`ZCVX*@2"!AQ@^HN,4JES! M5M!/<(>-C\*Z+U1W?,7&T[T M0DM/KX[-I+VK8Z@PD4Q#7:H?H('T3>;C;ZP`]#6(3LBX/?H$0V"F82Q>DRKZ M2,O@2DSO:KT891B`QB+HB"N;0NY`?D_W%A>_I5^0#NQMF_4T>5DI$;**Z^YK MZ97S??G6TP<3QRU.@0G!YB]UW#O2U]+A>>@+L4)AVUS4:5^[NK-M-)]+;-@\ ML7E7QL,-AU.9`Y7UL.[$=Q,$+VB@ID0%2'I$GY!EY3EZ0&Y&D1F@%H@[KRH^H6PO`-`QC^P^,,/S[U61XWD2R! M0U@X83GY&LD+8MJGB=S(5SLSK7>XS-@;/HY.#CT@$"2&T6;JTNVK.QRAK'^+ MS?65\?:P@=-PY3I^#O\&*($/M<>'W!#K%-O$]5$IVA9=GY.V4MN\(QUW%7=) MN_(+TA/M-JTYF-R8+$OYCHYBH5#,Y7ST%+A/I12ZG]5*.8DC?&HXDG86.L(A M(B=9.4YVE$K`E\O)#DGRL[1?]5'.?'I=M[G4*Y55P)=+(Z5CI3.EJR6R5.IE M_?RGI*W2.<384IDM]S8.39V?QPR<^;?03+AJT'-];C90L\>8GTD4B`US@4&R M[`R'$GB=NYN6=?]1+5UC!.1Z8+O;!O_)Q?J6^>AI`SVW]T"EP=2]C^&9\M'G M2`;BIVA*='6>ZMV0#78]^2.2L=AL0:]9OO&6[I8,T.OYN>WWSHP9`O MBQ;G7=9N2@I^*0!9DEN]J\E/><1WI\>_//#B:JO15;$?;/FB!O\%>Q$OX*\1Q4B2_2[U#GV08YG73(,NP MWS;/5ET?U-.!$^!Z!$7TI<`G?N`M?\%N1C@@;GT#DJ(9$VO$9HL5<#;>[OCD MY_[?/@080GL>;3@Z!D$1=4,93(`IL+]2:;BR$^P!TY5*Y0^5LY4?5]ZL/%]Y MMO+,OX4'W:?RE__X3`;=']9R!5`'F4"Q4(LI%,7TE2),Z(H7%&HQAO389VHQ MCC)VU&("Q7.UF$+QTFU#@[VEON36R3WC>U.;]NW%LM,38Y("TR M,3<@,3`Q,"`X.#-=+T%S8V5N="`W-3`O0V%P2&5I9VAT(#8U,R]82&5I9VAT M(#0T,2]4>7!E+T9O;G1$97-C%LP(#`@-3DU+C(R(#@T M,ETO4&%R96YT(#$W(#`@4B]#;VYT96YT'1=+T5X=$=3=&%T93P\ M+T=3,2`R-R`P(%(^/CX^#65N9&]B:@TS(#`@;V)J/#PO3&5N9W1H(#$R-C

Q7RX[CR!'\@OX''EG& M2,-Z\3&WM8TQ8A^T]]'/1D--,5Z ML3(K,B+J_3]^MMES]_#7QX?WCX]U9K/'W4.1+>IE76?X5V0Q5O2CL%EM_;+, M'E\>WO^M*[--1WW\UVV.#\6R"$6=/6X>%ORSHF%?'Y[R'\S"%.+>,>6NB6[I\:URS#'GV*L\WX^C_2N<<9,K>.+OT^9?.E/5U/K!A(96S3KCPG7UZZK\T,;C1J;JZSL3*EH@HV]62YM/%L!K MF;[6RU?FII3#E,GN#[+?S'QZ_"=GV"Y=\"Y[_#OGSE:>,F+AM=B`[-%G)J?AFMCW0>NF3MTW&X:&7A_9%RU]!*/:U4 M(W8GZSLWO%V,J_)LIT'1-RWG=XAQX6+>IY#7.I-C#;1NUW**:?J;"7SL!HMR MR]9X2RW9DZZPNO2?AA`4=PL-89(;%\>YX6SRRC2XRMOC]BX/;EDZ6X[RT&#Z MLBAL&*6AINE]2YOQF@&+L_,4!6>`S_6PTNX.X05.6\$=:QT^]-.\`H>+K+QI M=R>A:R=E@$&M8Y[D&_)!/M%``_C_)_WX-#<:UB0WI;W!S:7]HEMM+X!?Q)%4 M7!+3/(6EJPH_Y*GDFA6\5$$3M3Z=#H8R9?/L8@`##2WE0E[?R]SVR!EN\JV^ZVR=^T6? MQ'DNZCEP:25@8>Q/QGMJ_*3?O4<3XIZ@J;Y%TY%R5M&9\?\-ZGT&:#%91GJ2G+,F2V:5)&^<)IC,%S@%%<,UO0D[A1=D-A^1F%Y MT&(D3'FNQC<48>"DR2*;-N.TEO2S0UXI_J,.2H,YG#CZ0*OOZ<.]+L#!T:(D M!->ZY=S_1+3(X^XY3*.=\GNXR2QCQ=*Q,B6>L"4GY$)G3^Q4SE9K4_D_*XEQ M-HEG_K*G]3P>VC0S];O=Y3R[7QNP5>SSN%&,8.]IJB^X<`R3T\$1K7^H[%V*3%0 M8CZ#BL*M(ZIS;7WE+$1V855R5HP1O&UD@6&^J](XVK?T06FJ-'*%M:M<.Y^D M$ZS'&AINP'#-VIR&5O4-V'9"<`HIE[\0SOCT5MI,_%[.ZVE1DV8,%6JM%FBL M%6@=A!'NRW.-71+)T)-#I7J!B7U6KN4*Q,#4<=8.JM;(!J-'HCHEXM9PL;V^ MZ2"4LI52%OSM4*>>#Q'3+_K^@DIJ.,+H>5G][$RQ(L2I^-J[8E6U=)#%4HZI MD4`@%;L]BCF0G,SD\1:-X2K)026YZ_GPJ8SV1R7/9P-D#^]GIK6&$L7-/5>5 MUO9N?Y"Y+/:J',7*\G[9\[V'W/]S1I>E&OSD2L&CN[ZMN3!*<04>-2!F M[*C]+T9MG)\K$-W/),YX6R`$+)CARW]FF(2FAZOW+D/RWKX9:L"5.),%NR-` M,!>J=/`=0JY%*-KL*Y,71+Z#<,U&JSD9[4DCZ8GNE;)UW[ M.*S\EA9;,U/&.=ND\8WR`RTFO1\EZ`T@EW*KM`[QWE0D. M``720IF`6"H^9DI(K1ZD`:>"(G;MJI>TOEV2Z#!C,4+THB3BM1-CQDMBV(OZ MC54_`PMLP/%+$748;=3$_)2ZTNN\[W&L55_$9_!R2./K:>A%@!;TSYNR:&N&&8#$:!IFK`Y8]<"_[Q*=-CA1 MH%L%3\G\CI)+57U+QV_TQY;-P&%A#+D@D"L5-OB7].ND*0&6IJ+1SJ)P5+;WA#J*E=]3$E9!N MO5_^UDNOWB\3479Z9SW1_HJYVUY=ABN$@A^J(!;E6+[](-\UY)M"5'&6NXF# M9M4X-R^,'GEW62NMO^G<_F:*-G:&ZV6?2O@X<,CL!H)FJ-]PQR'W'P<$A>M0V9K/1 M$T5G1+"B5\.$&6JZOUZY9GI/P*TQLJ'NQ+PP*U&\(@U(\,Q)6[*#UT*I![&W M([$/(O96Q1[,;$7K(07/2"[O'`%L38`39<3UJ[4JPPH+.9`%EW9VU%DR4`J[ MS%-O?QH618I6TKXUWM+B^IB!!.*9U(OWM_4"LD9".JH$ET[1:2C<<9!F',G, ME90"J0K_>Z^DPYV3OGQ.E]'HY#KD1<3[L8;OI$-MPB#O(PLL`T[R=AG+>C,Y MTK(LDBLKB MVGOARJ(AG<&M-]OI[(,LQBSKE&6A066J:3='LS-R$IP=MEHW@P.T#3N_[J0L MN]D#@+*XIX8M>X&*_1V>[`G$"?+H`X.:!<$YI'+AI=:=T!]KQZ4C'J`#_,#1 MUDP(>&HO-+645-1\Z/AFVXD+D\`>__)_#R]%;`M[DP+L3,22HS[3.S#$:L8> M,`U@C\01'=03ROYFQ>"FI(.OKG8ICNV2&^Q2`[LDYB`FNVCE8-EB$ZH]HZ;` M(45V+HQQ^$UU6`YVR:K#LC<.:\9$W%?W'#R`#L(!]`0WF_PS+B?V/FS:5%V. MPB[B`(K")0W40TQ/VCFM=+X8`.WT8OBDS]K9HS,)G(PPA:CD?;U62Y(YU3D) M9;CH6!6ZW1J5VN#H6!B>$9F5NQEC$KWO"(SI]S:UR:5GQC"5%/7H=C6VFZOC M5LYBNE=:JB`K>54\\-]3K@QW$7YJOV";9`0O**8:7JD:8F?<-[9NOJ%2?'YK M/:Q6;-;%R,6*-8;;<,P!:WN-!AI M7Q;4LX!H[++M*B_$N^^&3SSPQ,<)9&Y-#),*@]>1,^WUJ M/9J9R^>\@9G>IPH`<%$".0X7I^VS4E0]X)W M%K2+2;QHP*,K'=;+!MZTO^W(N6VSLTX^Z=H=SM>J1?+\K5C+N>,]C3OJO#G_ M,T,/5FKZECJ)B5O@T^9?X"'3&Z$6IRQ20#">84J"K1OY`#_-V?H:F#R/_V6^ M2G;<1I+HK_`H`JV"R&1R\;&!AC&'F39@'VI0[8-<4DD:RR*MI5SU(_.]$^]% M9)*4Z-XP/9B+J"1SC8QX2P\(A?(?`(J/,X"A@13@IE)LY:2)EH3Q!_V8,/CY M;"N0:20MQ:U#=+)G>QXI&K/8AXAXLEN`O@RKV\PK6T!W^9!6M4AHARK^B-DG M<)@AN,;A)@O@%L=0\1 MHG]$F!<5Y8/.L+>1N_Y)7?$49C`X.MI*IY24_@8YJE]4,?1KMK:'BZUX_C4M M\I>HZ=Y*N'PH3&@EG!G8AG6Q,"N11=N71UEBHL04;6T*6JT(WZL**7^_CJZR M:QWM)&!/K``*1Z0LMU M9RY)=0^Y(D:YV[<3!G-4)5ADOV:)R+:L=^2DE=\@>/&50Y?A\HV M/N`SH,(U'#MB/=0C93`O!5MZ.>NW-002Z9PW=$(^8\A!5IT*5N7+>J#6ZEZM ME4.UYJ):JZG67)1>CM*+QD(*!\8B6P3I)?'C->6S%QM['@VQEZ<4];$+VO8P M$1IN\__(C?VWK54VAH.6B5//GDYV*@2_*!E\)&B#*M`PNTD)^54=<4-<-6-5%K2!+QJ2^?M#\;TM:1++(%V9(2[&C8#O9XCGC/5)[("%?0H"S8=*X*D@XH7BP".[UA_/$XQ=?-B/HH_XT0VYD26J"`L,T=J M;;_O4.:D2:TUO-E,W!DWB4S'7AI-W9E/Y>C[N>A*Q9$T\9#9`)?#@D?E=FIJMY*@9LY(:N52!YF;=-CF! M&:K9Y=-9!]BX,U6QY7VI"G!"$T\3N9'KZ"85[)4>C5S#G_TU]_4H/#ZO[\_K MR^&E%O%2*[U45)<]>9_.5I_W?GNWU+SI;=GLVV"Y' MH;T%INC#4#EBDJ%]06"=_HQ)#$X/ZP4:I(QM2SV5IOTU5+T,%+ MN@C?)9&QV^27F0Y[E4^Y=OTE-5XY:]=(9B(AP)G&:5/TXB:A:JPQ",BYN@:O MUZ3TO+:"/JD=F@A4E3=5+TJ+,HA2P!?F5G/:4(03*0HBH$A?+N*UQ0A2?1TN M7U+XDT_K\*:U;D_6[I:#@3+-:>+(W-45HXYMKE[8IKT@X1!)MI_"/=*;NU95]-CMCEI_^#COK9S_^G-;P?.]% M["+?WD,2Y"A3BO`#]IJ+RN`C>8OR*7%U2&;VZ/33=I=FV/4C8BC)LYAB],6- MYND9W;+GI]1#>@09%-1M\J"ND_IF M98F]Z;KVR`KRPQK$WJSG11^B=+UDH'YC$4ONMT_V1XM[M4/5E9HR<'/\N-:% MCZ/6@54$2M*E59!489>=?=[:VTR2+V$ M9ZYB$$[GD3+X(B@$%+U#@&,^_BRLAN(BH MD<%+XM1O1;\WU&)S$]"85G;D$3*YR,QQM;G##D]I1I!:25LOD8.?!2(RE6VA M>\-;R:!EDP=YG:M"P!I9FC5\L/4Q+6L)R9NTR*;8Z1I@IGC\@T+GJ\:KNV9P MO1YS=>8`/^G+3T/FIAC8ZH=D&^RDSX/[5+MH_!^_B[D\V$)=6,FZRR>;U1[] MSG21Z$,G'"KG"#/K`QDZV^GZ^^!*58UL;.KGL"UL=*%^IS!IF=%!R*YK#&AG`3[^^VMC9PG,73C"`FE_)V*U>@MZ6[N1+RDJB MK@SI8E>U&:47>W1;2X='3385GVTWEICM(7QA1@SS\TU0LV/@"`F1!2WH0$C8 M^0,CT,SN!7CA8S\F+XQ%-A,I=2LM757W&CQS59"6I>47=4!.7LQ5"@N\7KA] M*F7`3$U,A8(Y6)#N4[B:.MJAB`"[B>DYVMRXT&N*Y_)3U'+&*9OHP$1XE;)0,IYN;E?LHZL'-UKXW M#2Y>;0TT*Y_?JNKA/^+)(BD\`5B7>BV&1;7XAW=3$X[6J) M.J?/6S`AV;HY;JY%$`UEV>=&&Z,@E7%4#2"A9I83[@_TYGU*G:2\A0++)`DD8$=4JD&,GU[;'?&LR7P[I M#%@7#-`.F\'\G&?%R<(D'E?2IJQ)WLX.DXFE=2HF;9Q\/\?=;70&;(V]XZ[1 MSW#%0GF-UGG('^AWQ'.)C92P8TM`76;:5=V.@MS!VD*?@-;.$G?Y^#G\8\*@ M@[;7@AKC"^Y9D6#>>[/+.\V2`TFM/I*=3A',TG)#D(\F M*E%V\,8.I;)#_]G6($EPG+)1!9(PY]C:EZ,VD2U"TQ5%AWK!(:1YM1]XWV\% MG\7?X2I<%%0C.F<`Q\23U2Z$L6HL0Q[N34Q^Q"Z2#ZDZDQSV[#,LWT0AR^1U MV=_.0,'EBPCR68:"-;UNKJ#35GQ)2<_CFR)KK:87V`2"Y$:D*+YI#]A0J&;:D)QL M:E^B:N$&K^)0#%1+$=0NY<-]6B$64!1S?20F,"@VO@+[,E8J-3>"`B%VI[!: M!_&28)ZY3BGE$-4/-.L\7\1N#SJW5"\$MBUH0?EW(5192O9@,^;&$?2+I,Z)4U"0#4 M;]#MEST%?$9I)L"RLR9<)9-9Y2OEFPD]WB:`B47*%<(HAF>8;KFFFU1R[>KK M:@V:_I@2U-O-+5L+<`2VQ@CAO@__&DXL]R3YT?.Y@O2#B&#B>C4[JE$%&T,% M55H@Q12@Y-7"#2I")UIO.*Z`KR'?FY70*_LA&7\!2*!<=I4>NRM"^=F>K7NZT"86@SJ5)WH*F"[CA5$^VPWQ MH0?BL'D,KP'/"KY:]2MR&$:QY/?=96]FG71-NJ@&95ZJT[Y#,@,^2+QKXBNX M;(\\S.1TZ9QJV;0JUHBL+OVD7WT:B\PI^IWY6VZ6@Q/*L,,P8E%5^5>05Z0ZQJT<: M7Z'C"Q3U,*/;*`3J[3<;V1,B-?S)F2=RTC3^3+S5<;PS'7JPL\)^X[2.[\^+ M_:\,"[K)^_>5@AG;V[MF,?*A+\/M\\RP*=0,=JBUJ!%;J2E!:<\Z\#=5.7-) M.$2^P@YOMV[,&PVLK1J[ZX*0BWH>R$Y/+$,Y[$:@8@7/0@99/<.S-KUWJ7]) M)(JU9GZAJJ5492*#1WW]UEU-($-M4.%]J2_(;3-]KF[S%7^SNZ_C$/T0FY>&"A+N3L. M4:\_01N)&Z!VDJ(+8-P5%F1+6E>S_!LO M4R/I&]4SOJ)@D<,8)$^K1./-5?E$KJ5L/B?7<--<](D>08]ZB[`S3S.-JH9E M`#75L1!#F>])Z45<)U1K0NUC@DS]I*W#![Y85*Y$<:91E@RZT56RMK<_K1U* M7!5;\CD.&^S[YLQ&<+)R,.NB%6;5T1;V-G^%=NF1>P#D33%S^C-`)"85X,8_ MJ&M)#4Y!*>Q)BD&@5:=SHJGFAQ`()(JRGH?`Q_I632%(52>3MQD"#0#=[[5> MD<'I_K@"SC\;IX?5=,TTXX[_>P*F,3FEM:ED%6%,R')A#F/";YNPV6!'65@_ MDCTEX"CU'Y+5OM"NOTPX/_-W]U^>*%Z&[.*_-F&_`#9CW12P9NDFIE\7GG@YN4R6#\J?5_&(E0']0D<=_I.%BC( M`L76QGJ^M%U8\:B:8/.?E'NUN@UE'?`OHWB0`(6ZOY+@43S1$SZZPEM^7VA1 M328M5#.SC_IF3_L\DY-\#2YSYK+,7.9XT69R5497X,-A7U1E-J%(R')-_DD%+(1$)UV1!]>:BCW(Q7/T&&STT,D5 M($^V=UIT4$K?E9B..JI*SDD1!LD3@7P'#9LRJ.+2T?8/YPQV0K_9/]NZX69_ MJ#V#QC0WXL]7A!7JF@\;#%:T^FJC*YBE!^[[Q*`L3-S)K3WZ5M5GRD:(\0B5 M4L^;K]8BKCFA)K-WK/DMAR\J#J^6_8C9O!AZU9< M3:\*WGO-@U/1)Y:,FZ[L#$J6.KQ7+Z$.0I;\HBB(/0-7VBCD7WIRT(2C.; MTNW)!B4<2-)]DH8*O]T!I&[[>^(S=?7VVKX1YA6E2IYRT-[%^>2)BJ6=6FY/ M@WG[%"*]P(UU;R0>.`!"@=J>/W(J'[&9+6327H=?QTHVM1N4M(8XO(48/ M=4THQ\U88E(!YJ??D@R`>$^\-JFE5C7T,EK);IA*+K\\\)U MEUHJG7.MRATM#QZE&RVHI*+@[;+"LO/@\75*F2I8DC*T'GB45=KD\/W4W0DQXUE,"U(%`,WF_<=3&>MNEU=>. M+JGCV4_P[R.6[?[Y//'/Q(>XB^(6:@7=@^0N[#H;PP`9ZA\3P6Z-%BK73-V! M+\O("Z4!F]I!-DM-7B%D^']%!9:R_R4I41EOHOHPC?`>C[9*>*2.)9[S.2(2 MD>!)-->"(^==50ZL\`#O]X#-.E:) M+-[2-Z8),U.=4!WO]GY8?!\W[+RVVH\%2&E0R9RAF=J'!9H]QC%N#>G-4U/E MLUBX$(LB#XC/G2+;H6B/9_MSBB/`I]`&11(ZA$*U6$X+E>SXY<)F]G@-"WM[ MPH^Q/=/E+RHH),X>.+^I#2<+,4[70SO=66^UT[LL_>[F'=K59'F'(B.E]<8\ M**TBRA\1'+O":W;6T'Y/%.Z/G0J$%V(J5:HJROK_EWMGF@+]NLNVE[UJOP[< MG&EGX,);$(&0?[%/?23#.SIM;Y%=X.C2P%.OJ1M7I3-(I/%&OK(;O79*!;T] M+PGAM0]D[3)BDB92UD#ZL[5I=<$`S7(8>I4N@+1-W.OW5^H:76+`X*YVPK.- MG?0D+EG1,KS'O9;Q+I^CX5UH6O#P]UXHJTA2E?6/HW_7/ER3W MF@M>E5M%7U1L>=ND<.'3P1;JH]?!S4V?5W@`54OFO^J,+JDFEYQ/JE@'D:QU ME/Y_YX*\OBNSYG$+Q<(+$H"L;B8L^(D>C,-:@!N,DZE`\*PU'+LA.:LPN!_U MV4'8;3WC6ALE+L/`LG2=DE)&,\FE,U"&;Q5&/-%MMM-,+//C3W+&0+7Y.,&C: M(.>T($J#TZE:_+I2!M-:*L%?(XP`8-"_)G5&+/'!(4-=B_\*#(/6'(/GP7`J MLJ-0#96Q@53H3."=?$)S>U_U$HJ&;0]?F! M9"Y1^]RIB>1&_.E;?=HK38,0REB"=\X4=*5J/"/85-!%BA77J!8N((/&GS;SN1R[\-("X/!A6'P8 M']PN#)F+KV//XR>_9TY-^H6P@26HI[\FN.7FR#*=68&G$"V>M&#@X/ZP$4[= M'BA>MQV"P^EA&0S+32Z7:U1J=BU`/AD'=0?C.A7H#'Z^UW^+HP$GL=VYL\CT&O(P M1SN4J(JN8H$&B8'D7KQ6X7E5%]<`>"`ZDP[+7P/D9.%:0''= M"T$V[=OW1^):.?LA9\T!*3^8W15<8OX<"3MQMK@232J!H0Y'/1MJ[WS.:.#K M"_U*=FW/\M2\9]TK$L2AT@Y=NX=\L\&+>_'@I]2?'R;].<3WYG*U8,F`$9!]R!AV1RSTKNY4M[^^T,7"^Q)9RG M!WE#/?"74.IU/\("U9[=Z4$0=F`T<5+BR5UYU]T#2_!J%E[YU5<@,*/)LW:R2=L_9:87/)QW M.I-VV10@)3$)"/U*0>/!@&QCW_#J6D^5",2LF"B>@<:&PM+@+0NFQ%-K\V;+ M6J8%^ZH0,LG7';^V!&F^IS4[<%L?7+7KE/TS:5-2J7'F@=L['UCI_H4N2PZK M7E04,^4*&:?_I[WC1/"M-+D>8`))Q]>ZHOW"F?;+XI`X=3XVB5R;$%D34'O6 M`;1)0F<)>`.\#SB.G(N0/FP@&XXD`.0CNVNUZ9)K6IS3&[&&&AA&*FV67Y^T M,_RWAF\=E6]K%_HGO(',S%"Z[7>E/HW+S[^E*B?S"L^P2"E`6G;:M7T=#5W7 M&MQV[&?.P_CK;7MCOP?0HBN9/J$"/T5XMBX0';8N),H/6B57+RJ6ZXV5MD+^ MM0XFYTR89.DRH##MMK/NL5?U!?^#MJV&R%K9U1K#>`""_=&:I-%IW[/?F*!A MA[O6VN#1><\^>7B1&17-1\@D],[*$H$GJ5O[*YE#(XV1C2J'2)W>_M> MAS5X6,$<7(QD0^!R;>)H6E`CLV1S7*R5[QD9-/:W4.1.6OU=,,B%]@D-V<`) M[\S@Q0EF:L/8%2`+7/\D!]7:S#G>VS[?[QY?N!(;!RX]':!7HGN MEC4&"*A[(&!SRYX(Q!%%:#4C[H(-%YC<":L/((:K-*O9:CB[],W?+AY!]%K= MA`EHCPHUR\8&@'HQIAZ45C=*LH,P=1VE0A2HV%G&;FW]8T(Q@IAP)+U@2@Q&087!YI^;GYT60D]3! M4J3<)1;WVH4%UB4(TX^MS:^4&-T?P%FN9CY='OO*R!ER@T^@G*6OA"#.53"1 M&F_L^X%O+>:_I8VF(*?[1Q]'LI8&`'-EGER!E=1ZJ`OAMU80*B#^L,6GHSNS MN=="FUHD6;\)\=1#]6!"\6MQ\?>4Q/J8&K_FH"]>=->*AH$Z:^9ABDP[TF-A M`@LX%0WWH/UNKG`4J=E:@&U^"G*,/')(DP;7)+1UBFE+H0=`#Y!`;4D'?>C$ MOK=4>G+R>KICI+/5R1HELLEP!DT\^+2P6%^ZL5\_[1*W>9ESJC,D4U97TQCE MUJ:B:@YY)A(A>U:Z+E&10=BGG92E*)HD\$\Z7R$^4!+4%T=>BRD#^^I7OPKJ+P)@'YUA[ M"@W!4+,&:E(T/7:X43VS'T':JWR_F$?CA,HPG/KDF:M^8N%;#TGK?V&M M4(>6F!LGYM=FWH_Y#CX(#V_I1W--+?#VT\@.09757_X-")4&62?\;YX$B7!3 M)J$4("KG8N1)D[0>DW1425$;:2%9M;;?3@5#8KIW:X+7=,03E54&%+[)-6-# MF`+/<:_D&>7_YJ^2E?'].ZTSV M?481%Q:?+W^^B`*&<,VAO6>5)<<[J">27FTE;/(="BWRTN@S_DN%4LQ^(0XT MOFK3]:C?X-,+/E9DVLF=I9C98'])]:E))C9W3)Q<9.Y77V#0_N'EI[<^](8, MO)1;-[.7?Q\MZ?FO4I2]VCTS\MIXQPE*RDB!59NVK5%@*2GOA\B.961`[\\$KV5%@[D6:`:D^@YO6LR^R M,M)'CG+#1SXSK11124U5Z$O$W)IKJS3VY1L"5Y#U#-$`+N M>&L+>=S@D,Y)U#*<=HN-65H.-CX.%[@I$;/?[-=/'=QX91-K\Q,*+Y`HR[L, MD6K'6W'5OU@U]27(>4:?)',^4L.Y]H@\XBJIV3?T*-[_>P(J:)V/#1W!G;/ M>H8/MYME3V]RA]#Q"0F MRRGM'%EL488AU"XQWZ<%"JP%FQ""TJ-#`JA6RA($+/I5NUX_ZVBK]=IGD% ML+'#3ES003MLJ3^G_IC/FY,E/^'E<>1M,7C7C9KYD:HNZ+LV5(Z]\_WY?,@MZS7&F\'C@F54FY(M+Y?[CD6K+38JI0JU M@@VZW9+X*G1`^5MAC*^@RJT:[7F<>")P-V/*`SLBL*,8&+ZX$(M&(%;N5A=Y M)I!\6&S^5*O>'41CWDQZX[)%^N14;[F6+"C!\J^IM+I&L)>SVW1N/C2JZ;CV M;M@CZ*9,J49X;D&14(CBJHBVS;)3*YTQJ5N3!8OAF^N/QJ2^>NGB'RYP8S>8 ME+(&/@P$.NIMWH!UX?5>TE667 M-_;UF@]3*`L,>)>O]IUL[81[="E)9MX*1[5+M_7$9DS\9_HLTOE8X*TM]Y-] MEXM`/U@3@,R5QOQ&>SUW80[[&:U]K_W"$W08.73PP-TQ[[B](-J>?&[NMU*I M2-BGM&9'HC#H=7:%CI7/%@>\.(*S1PYJ%.]7GF_TM^./3*"6N7UN&-/^,S]:C:Y M^@_?5=.<(`Q$?P'_(4^M?J0Y+>]!Q.7^(&KKUE+<>5`=P^J[I\3GFT@)64K*.5JZD\%=G'4D MJ5QRIU=(%>*S%X6N)EJ/'_*]'V5@R`IN:2G"`#$6FXDGM6-46\=IH`]QI4H- MMN+C@%T6AGMAN2\@+[!/P$!=C'J\PW.9J[SU(YW3'-A:)VT:V?4@NW;JM6XW MKWCKO`;35QQ-`O8']@8NG]M8#B>LMNM'/$6DOV905?H/SP#EN=Q'GG$AS'B& MJ#8=AA,]'U=TCH=TQ6('T@059$`=3/^7&?49D+&B"P*7`]P6:W67#DNJ`<@# M2!P@_1#]6X@G\XSZW914,;_\K"<)D<]*5O<1'+;]AI76>,SP>MM.IM/%.RRY MDG'&PN/*$24J87VVZ0623Q-4^VE\F^6$)$(*!1=>3E4#W]8QG<3L(D0T\.N9 M0#9$WS_&Z-WM+O.UQHY?MS)*O8=7)\1R?W<.QN=&@O!;?%H_T8NJSX.P4F3` MEHD90+:-<-2>E>,N1EGQDI$D4'@;Q'X?:;HHI72I,!$;H9?`J2^`^D7ZEI%Z M>LNP>S6G9J.\W7Q.3$\[+9$8?'JO/6Y!/28TI])SG7PGUGR9!,`6U`C\%L[X M$A1G,!4D<5<^ MLAA0JHR1M!H2Q8]5$6M3;6JT$U-KXQ!>+='G3,W85(2/3M^9N^?<<\\]'[]S[P5B(DJB5I+(5=T8:'ID3>40 MHF_F$_'NZI7-RNM[?_@^+,X0R4I=TU.-NYNWQD"^@;'QJ8:6NL[*["E$PUU$ M^5N"M8&:C^9?/D)4/@-[I@:A2!J7<)8HL1GS,<'&YE6]&?&?8[X+\W<;EE4' MRD_['R5:`/_4T!A8U137DO`;[$_'7%D::*P]<6KP'*+26\C'WK1L13/RQ%?Z MKKG>M+RV:>G-;\]"`0U$\>?D(*5C9&!8I2Y*)3(N8%PU1[C*N"LWDBU\VK@H M38(W9W3@RZ$EM(XFT5GX/D,R_80.42%[H#]!*6S#RI.TB&>0A[TT`%ZKZ>_\ M&-51)WU,FT4"-9(+UDZ:`G_IM)!ZR$;U1IB*:26%J)T.8*V,VHVSQA5$FX1H MRV@];>/1D#OI*%WB!J.',JB0EM)!NL`SC0.PLR+2;$L6LIA.;OH&S8?G*EI$ M-?#X"NVC<]QBK#=Z4&$LXDVD7.2UGPZC@CL\A5ND0NDEK!2"WJ'W>"`7&A7& M+XQ3B#.>"N#+1UM`';2+7J4CU$=ASN8R[C2>-I8;1\B.6$%ZGC;23GJ9?DV? M!RT$Y@=8Q^A5Z=`F+OT1]!'])';.$4'HY(:8AC MXS'\,,\!E:`N+R_G5T"7N5>@*"%$MU0L;;>0I4W.D5N,AXP<(P_T.]0@`?D1 M0"F7'J&9DC*Q-Y*BB/75R,3$IX'OJTD!]#1E6\B&NXE;?S]_@(Z$U^BWOXS]S+ M-_E.)$M9)*)KQ:),5(C58B?HD#@OC9-N6D9;LBPNRT7+!W*JG"=7R2_*!V/B M8]^X>R/<&>XV+,8\H]W88YPWKE,"#:$IM`"W8#%J6(8:FO%>;*,=H)V@O<#R MISC)AW&.CJ/'/:#3H#/T!Z!Z&=W[`/0WG+$^U/@9ZDL`QE$R.YH:Z6@!SV0W MJJL`>;D.9Z.)G^'5H'9^B?<"^5?Y`$Y6-VJ\G][F*Z"_\#54?8OOH.ZA(ALT M+U+SX^(YT0IJ$S_`">D4)T&WI6'29&FA]+C4(NV2#D@_DTY+U]''.DO(LL?R MIN6<3'*&/%>NEEOD#?*/Y"[YC'Q>[HT9$],9NRUV1VPONE*)WA30@U\*3MB/ MZ9<4%"M%-UZ$T63!7>_B9OJGB$-5SW`*>MT"]+)QZ[_%:RA93!3?9P=ZM$\N MD7;B3+R(MR(/-_82[E8Q;@CJW%=;I:;T=P2&H5A MQN#^-ZN!"O,];"QXS?2Z.1V0MX'S(ITS5NK'V,^I!-R1@]*CTM=:1U MQ/!A0U.&#$X>-'!`4F)"?%QLC&R1!)/#HQ;Y%6VL7[.,5>?.=9IS-0!%X#Z% M7U.@*GK01E/\$3/E04L7+.N^8NF*6KKN67*R,H-F.!V*1U6TW[I51>>J,B_D MK6[5IVA]$7E^1.Z(R`,@VVS8H'BL0;>BL5_Q:$4K@R&/WPUW1_%'B1*<#H!- M+DHT'6LT.[`Z:`4S+3Q:JNKV:"-5=V1-LGL"-5IIF=?C3K/9?$Z'QK.KU<4: MJ87:H*S^[>8^!:;E7L1V.NK-_&ES4HU:LUEWT6*_*06>\&I2P*<)OQEC<)8V M0G5K(Y[]T/KE]`O)L^6^14W8BP*UH2)`LWEN=.HW9X$MF)54*'`KVGQ>C=M\ MT20BN4>KJ%4]IL:_1-'BU4(U&%KB!^94[CV4ZDKUJ`&W3Z-2[Z&1KI&1B=-Q MU+IFN@V@''7.9/;3Z%JO-AAL_'J+)>BY_M#R5/PRY-MB>K2N@30J/4OAL/:@+]FAA[ M\B=DBF8[[YT(K/?+.HUSE.@47^K].7.[3V>C32?WJ*,43]*B)[$\WCP.]6[L MQN1A!Q29-DB9#J4(61>9?5-"2JBX)J04*4$TW&*/<"S4AGS9**?"6X_?1[TV MS>5+NR?6^GS3X"?+]&.)^`GYX&%)OX9OJIP]2MTBCC`4=&YM32RU*K:TDR%:E-M2,OG1JB).%Y?M%>G M2?\=X$)X0^ZFI>>#+C2D@NX"`L4"\1E4FMQ"M@[Q/[B&[7$DV\!*, M=%.V7"4;]I1(HZ"O)'OL5NA[(KI"<\V4+2MH#M9R3#F.X`,<_C9A%,)W#M95 M:2ME@N>`3X`^'?ILS&VB(+(_PF->B\I8Z(CIB!7#=+'YT)R,H;H(@:7H8A/8$%UL!!NLBPU@R;I8#S9(%VU@ M`W6Q#FR`+M:")>GB!;!$73P/EJ"+5K!X73P'%J>+-6"QNE@-%J.+[X+)NO@. MF$47SX))NF@!$[I8!<;1&6'F&C8GXW(QOUW,2B8K>=SAXXXQ_&_FJSXVBN.* MS^S>Q]['WH=]/M\=-N/S^6RSYK@S_HI;@]>I7;S^`D&@'+VCCIV+(2:`^18B M#5`*M:T8(=(6T0@L(%%;MXIO[9IS0(4(MP0*:MJD#8UH@QJ'JFJ=-!5)R(=Q MW\P>A4KN'_VO*[WW>[OO-_/>OIF=G3E<%^;:890X)T!_ MP/3KC/%K+@'Z`O9UIB'F=[$/0EZ*=A+N2[HA3`VX;I4+,AU%JX<7T,] M2,033`\Q;91=/>*U'O&5'O&E'G%OC_CE'K&R1ZPSX]_`7D'$2:833!?*EBKQ MAU7BCBHQ4$4I?X%-KXB;F,YA.EMV1<7)J/AJ5#P9%=NCXJJH6!`5Z]RX#XX& M(OX6T_N9WLWT.J:7,RTQ[92=Q>*-8O%$L?B#8K&C6'RD6#R'[;"=%;%9MHV* M[XZ*1:/BW%%Q=([X"KZ*[-BFVI%I'%_%X)T[9R-)X4_5F`?@C@;_5&.Y`!^H ML2#`^VJLD-1Y\6T4$Z`^^#T4PZL`_XP&=?3^C[B;HW@3=[/[MY&$@X`W5.D< M-']+@]]K\*8JK0%X796*`:ZK4C[`KS1X397F`OQ"5?(`7E650H"+JK(`X(*J MA`'.J4H'0$I5)@'.:C"BAC8`J&IH'SF/AU&(&X+P>]68%YX^J\9R`)Y18Y4` M>]38(Z0NA'>B09;CMO0[;(7[XX`]@/3=-J,!YM^$!IA_(^YF]T\#4O]3N)O5 M8CV<-VF[+GAGBIVJU`1AUJK2?("HJI0"K%:5Y:1.Q"N1PCI[#"DLPQ5(88V6 MJ:$AH"U50Y.0?VLZ_Q8U=)W4F7`S"F/:2D%!QFY4@R>`79H>E7!Z-$+I-RB! MS"G.0S(;E2)80R@&(4/*"VCCD*]*1P'\JK0$($^5Y@'D:@/@T2KO5A7Z+IFT MNN>Q`X58>XOL@OB?Q0CY-%9`[@Y.DD]`[HS32:"2#Z44#LK9Y!_2)'E?6DBF MI%+R=\E,W@L%R%L#YV@FZ`U@Y&61-R0G^:V20:X')\D$S+=+L1/DHM1!+L`$ M>5E.Z;!L)S^5RLE/%"L94C:0'RGT629Y`=H<5XZ2YZ'=<](&TA?4GN^7?60? M3)*=T,^64`[9'$KAXV-D4ZB"/!T&4R7=04ANC#P5/$K6!5,"I-LYD.*P;"%? MAUS6*//)2H7>FXG1(!&>D^@ZM55;V+9H:UB/MK!MUE:M3=H:ME9;KM9JZ]LW MM*5L[<@2LB0,W8V1KRCY9!%$&E))#4U6)=4*"U\62M&B109IT2K(_%`Q(8J9 MK$P:OV;\DK'"6&Y<8"PT^HVYQARC2\@0'()-L`IF01`,@D[@!"2X4C.WY`($ MZY;+X*!@T%&MXZBF_RSXF7%8X%!3G8?K0P+W'9"#(`=`]H/L!?DFR!Z0W2"[ M0':`],W<&J&MQ[D^;L^H0S/W<+O3#W=S!]/606Y7VMK%[6!6"I#&!$PV(;IG M&<;/>=P[:CVU&8N=U5^MGT6UIW7)@\OSWQK,QGW(Q+G#WX/_^_"/QUNXRH;E]#G>4A\%6@NCH4&N`F@H1@%H M?#X:I#0TR.[D8R=";+C.6UXV[*PMU>.^O,S>(%@T!1@I22+`D"(1DL8>ZB M!^Z0G[F[-7>W%@,_\(>UYG[-[P=_R?_3E7CT?VTQTG^K]PP]RM]%BML[^A<1_'QQ/"M0*)^N#=0GY?L/S.+^PQU]P?JD^A, MPV.KDV?D1+W:+_>SD]I(VZF6(_\1J_??L5I.S=+9*=I9"XW5=F06]Q'J;J.Q MCM!81VBL-KF-Q6I8O^+1K0]=V[=MTXS9R[`5L0UJ$':S-OTZQ",CJI-S]`8" M/P&=D?#(K-<1GN=\)H.18.058!5;,.+O6@:?3MN=FM;IFC;'QS6MCND:5%LS M74.E-%+F]#N+0(+ZOU[^_$7]NL^.7>;?_J(0OO'3]P:X'+P(>5";7'(>G?5< M@9`>C]6(=#H;\EB$3F?$:K'HJGW9V3[7)9O7Z[ODWQAGP5JGVQH2];=;IVBD M:6=9&79F9%:YA433>'-M^H/'0O7-R9$53EFC5KU):V_=M>/%08QODM@:OY9JY9DB(R'!. MPCX]\NKT*5PVXM_X!,U@TG$;A5NOET8R_5G^-?C#>W:N>0JQQ?+TS+MX&M[+ M@@KE3"XB6$3(7Q^Q>*WBW73K^_FCVM:ITLABS!)DR9Y.-#8FJ-Q(:);6YP&$ M^%[]7N1"VV7K2]8QZR^MO[-^8M7S=1DX#@0S&KLMVNXWF739]IO>#&;IL]A;O'^&$=UKFSPM?>C,.878NC MVEJHYD?QJ2_P1R4EI1$4KUI86>$LAXI"%2N"94Z7NRS+W_O"ZD#86^ZOYO0% MC<]/H]*5._FL%MEI=I>_\WG/YF6EVGQB]>`O0SVR486<(T0XHRWBLGBA*LZ[ MV5`82[;7X[WKWWXX/8\<4XX'Y:F%`F54/BB0XR'[])-+&A/W"T:%[TAHCZ9_ M?K]\/)W/^N_K#X%5`/;?Y*YON[#!;+#,,U6;JLQ-6#$IYO7F+M=V5R_N-_69 M>ZU]KKZLUU`&Q_MR!),78;?9XEZ48;&8#SMF'%Q.*$,03"9!R"DPFS"G"UC< M=H?;(N3H?#K,_<&,^)!WQH=]*?Q=.BZNR_!6+,?TPPMAO,!JR7-GN["P_YH,3SO%[_R*\W&*CN.XP/F>VM[,,IQE:TBZOB'08O?AE M\#FX8<2,+NKA^%'RF;G"Y'.XII'>95*#O_K@_N@ZM:[*"C3(&4H54S",_"?, M$!D2;\!&]2Z3P^WH%X;M1QQ3=I/)\;QGL&:_YPOAGO!EC9E,8+*LJE1"9M0( MF:[F76E*B0ZF&L;2@$WKZ=WI3]-D.BTS2LK*X-4IKU>V!/)@UP=.9YWHJNL1 M\_B.R2:U(4/!(K7];%-CJC"+>-TK?81`HHQ@B^UM1;3(Y6X5.<0.+I"T$:9F ME!<5<,7/*>C73&L[B0Q\,W3K_ M_)X-/S&FC+G23OS\D8U#>B-P>E:]N?<[:W^F$:[0%N+FEJ"+TFK673U\JLHE M:/WGWO\S/G=P=.]8;8NAE;[KJ1L]<>,;=82!O+)ZX1K5!QDBI7ZL]^[D#]@/ M\*_XOV=_VS\2'%'>C>29B-I]1;@L_DV\(\Z+O"`(BACI<#\B='@WB)ND M'=(^]Y#XJGW8/2P,B^/N<6%4.#$"3,YXRM2J/;'FC7-_^F735H"/'EL[F'FI^T=3QM5/ M/K]>``F*.K*U33&4TUO&C>\;?_G[Z\:]S4V[&U]M^];$1=`%UE[Y(U7)'1_T M_5&HP2J8A_T;;1TV?K M\QSSG;2=O#WOXY`^J[)E?68C)"4&4C`*<#'EV*'8\1,8ADHJ8JF(%OG^WP=5B=VE>0YA&37*X@ M>3-%R8M$X\V4VKS2XE?E7U!'A9GVF0+Z/E3,E8IHW`.VK0*O:=D#]+A(/2@; M4R@+"R[05$(J(X"R.=JZ(IPE3S?&?_.OWJ8S!Q5-$X;//#KPT9?;6M>7_J$1 M[M#F16,:WYPZ$5]NQ/"7?U7J/'/<8!])C5PU-J$@`^4<>Q]J*(*=U)DA!\@Z M`"8!"3&J2CHKM'3.[U=86K:Q*097,#EL">>!J*L!W2O*2L5`4L"NV^'"IMM^ M;R-L45<@0S(1];^*F47QSA[Z+`?QE!"*@ZE$>\K7&V,3=+0WC>P.:YC[\TUU[2L%%"MF@RP0I_.Z=ZA8C1IP8 M*W6.CQB1K4VX5M'1ZH7K)AKB2&+UV*2N]?&O84>Y:3!52]&P6UAXNM:#>?'' MR<<=6_@!;H@[6O,._BXW4N>,MLA*-BPGY%`>^'0Z0LM,GTVV6E'N,'TFE#M> MHIZHKT]&8[&H3`@A11'8%$$(J6I:SH/:2>O**S$`U=0WH:1=/4D4/.D4"AYV M:A8&.09#I\1!5%(;&HP\S'4T-K]*GR73\3!<&H6O)Q#+-\$`RH`*/;<#N#D3 M68XBL/I"`60.SP>5A+V21%/G?G[WY:2W-?H"_N'@8RN-3W]K_*+P(7Z5N''U MVM;Z5"6+WC,N+6#&KN9@^U]S?A[-QC6#QES-AFO3((7?K/@1+T*.`NQ!3^G5 M+'2<&D;9(BS-/BXAN^$O2Y&D`!-&<%M$0H02ZYMD16Z,(L_CVS$I!=.EM>T+ M9!78#."YUZ#NWI!^4`QN--XK)0TH3\<>7J'VX(5M:MNV;24-;-=P5ZB;N-D= M=)%PEWRP9U[9M!Q-;E#N2EZH=P^V>]+#.%MD*[JZNG!E?Y23$5TI3(;5#6[/ M8_%\[-4%67%"1V#B+O&P>%PDR\-8=K)C)#+_6=F[%(>Y0@XZWRO!>H>VWIIB MBS.HRH!%@W]M_^@ZEMRL1#>HF>5PVA8.K5^UX_Q<=]OZN=X'1ZM&/KQ_OG5E MW8]GC#0\`\Q]1 M/$4U3#R+R7'D6DXE$[)%C?`M\%HBX5$YA@#8(F&9)\@X9R7]2G[AF)YD@H$0 M?)PD^4#`;Z7?"H)@2`V!T!A/TTPH&/#;K`QMD<.,-:2L].=!5G?;[3;:@EOO M!^.Q8$`4+#YYC./1W58KX21)H+M-I"JHT%.J7/[:R@,$_I9N06V7WSCD<'UM MCH+-+V<9AIT/?=5BD",4O]@J51YR(+B0K0V%F][,RERW?1TA5S;+E%F4; ME6%+%BBB(F!NX$9((QXO1(KT%PE_ MI;__4%WVL4V<=QR_Y_&=[\Z)S^<[QS[?.2]^3W*Q+R^V$SLVF(PLO(1`A@ID MPQ!@T*3`0B((+6PMHH,N4L>0TA$H'4M5M**IB+5=U0`JM%UI*1`8[Q+M8!IM M04#6M:)A#'S=<^>$%%F)[5^>/^*OG]_W^_DFQ10*'V2SN9Q):H]D$N@!\QV& MS`(;QVLNSB*,EED\B8U'CRYE&.A2YB35Y=0ES&&TNZ=A444`O`7?-S7W@(/M M4^(/-S)BV7-J);P0,;3.-ISH]!.1AZ_")1UM="3"QA8]F($W/?Q\47`RD<-F MQ,T-B/_^@]XP6!%6C`VDE^^2#N.'J6/6$SQ!XR1%L4:!EHB;V"WB!G4C_[[E MGO4>/^JX[Z0IC")(BLPWLD8;+="N`>L`O].Y4SK$'K*]([SC8HU*D8%1['2Q MH;B8$T<-]TUPON%)`S0LY'2\:%!FL M.^/C8U$6>CT&K4-P-5B.8]SC'.?%L7GAO[U^E(=.O/! MB5.@`;B`]:5_@R;0K-[NO_UUO_HUL?+XL/J>^M[P\<].`Q]H.'/N$;_@)]$> MFU#Z[DIGIH,%H%-<5]!K[Q6W(K3=*GY!F%;`'?:=XBWXA3`*[MI)IBY/\K;Y MD&_Q;=ZB.LGC\S)%+J_%:')524\5FX"IR>3AC8K-QJ-_GS(L['(<=5Q#)JLS M'%TT:&$>9[B,!G$ZPG'Q7B4C9#7:U5Q+MUR=;&L?-03P:-U*<*U$,./[!4^G MEBS:DHJJIN6-/_XY[`=&8%VY,7/H7;1H\^"[P4G#+[Y16)Z]DMU$-JTV]*U- MY47^?&;YF[$`JV[6UFR"YUY#>I1@,K8_G6GC7^`&S`:C>:L9&NKT=<'K)-KG ME>JD8I_7((DE>%#FG(+C*1[P?(H3!*=3X@2)=S"\771ROLT6_:@8(%5 M<)/:M6HF'H''5GZXOG%=F9*]AW1K^OXZ+A+;L#B6P+Y)!QS^I_,WF)]AD'K< MOOS+>;>8&]PHET=S&SB8KI/BRX%4CF%#$+X53T>'@#G-EH?33DE<[I+*)?24 MMFO#F>7F4IGUFSQDE`0)#_"30/:`4K_9A./%"F_`E3"=,"02K"0M_CT)R#NL MK,A=LD$6DW&LZF4/\-Q1V"X6LL[ZY!"`;[O[/D5&U'(W,VLD>O'# M:H6<*9/1EU%7%TN)=T3A[BG`ID1$.H*(L?KDHY&QB2CDC(NO*0)CO54!B'VB M$00^XRR40T9D8,5`+[S0[4&G]"GI!4WUU=>VO]@[J>R76SYN;;U\M?N\Q2-2 MJ7C9F9[]1O)STWJ901Z1*!K@??@*M?_OUWLQWM MO]T!\*G!$K5A]S^[6Y=45BUNKIFT]D^[U1&'8,$)OX?8B_(:76^"1O?:@;V6 MKEY`=!*]M@$;WEZ[!\M,O[@1/>,2&3F M&CR&RW,^RV7D93TC_5@`VYSV=4K'"R&+L6"Z:9ZTUW2X\,M"$BTSZF6.IB=.2S^MUUTG^-J_;P>"XG^X:%2X`@XW8PX)9QS`H>5?*4X,EK@U M*RL-3N0?^BCC]PDMLB.>XT;M0X$<&SCL&A-'?Y!O8[:>&_GAQ?5S_#\Z05]YU'LD_2Z_]+`Z!0Q$=AE9V5`+/>6 M^Q)LPFJB3:809ZY0PHKDT"II\J"?K$Y@&A1H#Y8D9#;Y^&]*)L8!09<0F1E?P\<"09T4 M)B;(_R;`G`0Z>@'M#-PTH]9H'+'>AJE\1^TTN&E!O9F]R%PS4K(X':Q7Q)!3 M71%3]S%J7UR=[:I#5RI"NJK-7CX;@0N(-VR^(L2_I%!NBE=G5\-7N3)GG,]' M8$9:BYL?A`SO/TSCYULKJ.I9RQ9(UI'Q,BZ.Q]W;\[;G M[V#Z+;124EQ='>)XPAC&<5L);\-M86!#=,/U<6`#!R0.Y'&`&^2,"F'#C>A4 M==AMY&S%%$87BOFTY))0-?`%ZS!,2L0#?DK[&^XR:$SW"=498,@%3C2FQW700&H-2;OP!6YWBZQEG,>AGKJ]RE?!TFA@_H.Z.WND.T:A:D*9@Y9H`#1W;(FV^6.V_(A^__O4 MD["#6(V9L<:TCSQR'3[OH4Y?-S_O)2DS!*R9LS@<(DG]#)UU,I9S[J\.@KV8 M'A#)68A@6QJ73_U*8UB4!+.T)>:M[@(]/FWV>E#P?Z;+!;:)^X[C][_S^W$^ MV_>P?8X?=WZ><6PGL4V>OI#B/"`TT#AIG(526K*8KJ+N:)CH0*$/(@H3=.O& MH*@=L"*%T15H20E[15.A(+:.K:B3I@*;@*Z:Y'6B]`78W?_.AE:R=/+)TE__ MG[^_[_?SW0:N3(TD/-E?5LZK#G2E\K>NMD=[Y',7P7.]\KE=(J=\[RKR+*?Z M_57]L[Q2A>@)1#[68#".JI3RL2?!D\<.UHZ%IQ*U8^^=FI22!7I#!"2]YD4' MLYY8?@I@2FDT<)A`" MF!)V":AP$GU8Q+LTHNCDUHE_$:^(F'@277VL:Q'DW+&+EX@R<7.L6+YV07*# MHJWJDVVP+Y0R=]%/]@CX&6540W+@#^&@22,$I=4'XJGH-1FVJ4 M>*?69!GX8YZ#@I2?@20`GT9LWA4=A?9`Y?M`!YS]J]/=&HT!-_LI``/<`(F?HYL2>G MR9';J%GF#'F&.LM<)S\CM5[29XO4C6O&R7%J`PQB#<$#-^_B6WEGG=%M9WV?4J<2<-:"F#M7[<*+A$-W"?1%=5$7KL&X:&<\Q4N1#(^'RW MHOJDS+E+T'84KF=C@X4B$3B@H)J78P>\:?$-%H;[GUAT?SR\9/CU]RN?GEVQ M.;V_KCZSTY>]?'[_QP]3Y8\4^\NEF"U2N7&Z4BF)3>L5E\2HMD'*6N'K?V%K MH?ZDK-TMY@)4Q!/V84/FO"?O'>*'?&L]:[V_I4YY3I/G/+=X`^D<\H[RX]Y# MI-+@!0&U@Z4U1N(-)5`J:8*`2J-[W?I``.642AW:*3J\G["`A0.8#5G%=9#K M)%E)J0OO#>_N..>X>0FF3$U253G%QN`(X$=24G%,;A&T+!D)S^ZA,&F1TK@F M&S39A#3RZ(N_6](2K$NC=H?WH8&?;UG>S#4$'MW:/7#Z%M!>JL?.;7XDN\*O<6]S[Q)GN+]S'W'_"7_! MW0ZS!,QLWN68XIV\V^4Y"7`QP+N="@P%"I[V.2D%4*IPVNQ`5(-F-3X8"O%Z M_FE:8)UP'=^,ZL2(-*SH`JEK$I^WE:\C4M6J*861E`)C]P)"?%:Z`V3%R'LG M.P[/U?P;L4@[QE2916X3.%`G:RN&9@OYOL>#%.DO5.+_/K`\$VQM6PGFXMDC MCVYNB2]]\&>7AR=MX(9]]>[E+[TR\"(Z#.PA6P?8T.]7--P>%Q.JF-G,3[?5 MU5?^(7$+AM1#+WL$:LD!TY1#-H@9FO0#P99#.]C)Y3KRYVIOV^X>,=@2>VC3\L+NRI=H'&U:-M"J^!'Z1Z!R=V'7H53,MYX827=BJ?0T+PKNDS.J#1:?4VG5W?HE,B(2*$!A`L MC;A"K3Z,5X88UN)A_0;@53[A<:M5JE!0!_T76N\:44N97"87+VBP.705$H[= M@??Y$[S7'8FRJV&?*1&;WK.998^`<'77(.3NR"<;DTV2-=#WG+5F&>9&JM8A MG9GTY&0T=WWC3'=K(AOU40VIX\?;"^5W$\KZ7G1O?NG.[QQ9-]J<%:/<$HT= M;UE5^2)?WKXVKDX@"B16&<;>A_^K`6&1022'?"4>,K&XTU"GCZC22+^;=3F= M=6R$3A/]SS<9LZ&AT'#?FM!D:&MDZX(=Z6T+7PH=BAQL.IP^O/"MIKGTE^H; ML&5YXC93;X_;I<@R79D.;#&DCI97&9!A0(P!)DCJI2RW&/.WQ+4M`U&M/ZHV M^0=,.74NEPJZ44'EL>Z"`EF:79H:5LVO2H'4<.?KW3PGL%L&.PWSOQ".PE0; M'HJ]\\%8Z29,K\FR;1EANSAFZZ\&ENW2F+0^YIJ(RE7`+6VZ;+M6NELD+57L MLC3_,-;N^'-UO9!O&S):+03PBU=*ND`JG90K)'S6`SG>:`:"AQ1X\L+QU3QD M8.64Y4E6$P]&79YTY?I;VON6IS9,3SW9M_W^BLN= M-3T6;C29=%B\?M<8CC.V2,_01ALN[%NW8]9I>CPXT3[?'4"5K#/HYA0HAJ+N MMI?/+@DZ8T7%;)6%90\,(?/B1DI/>5`]K6=0+:UE5`%5T$[;&3I`!\-TF,G3 M>:9`%YB)P$1P#[V'F:%GF#EZCJ$)C9MB@Q@==/!6YMXB*'B7II4WIUU4BO(^X_C][LX^O^?\=K;/SOE\E[-]ML^OY$)L)[DXKT#+ M8`1(LAK:4E)`3&O0R$JJ51&"M85J=*/-$)I4D(!-2RNAP3I`:&\J`3:*F$3H MT*96&B1C52.A*8NT0=S][FR2H&J6XOA^R1]^OL_S^SS?KP$8%!2X]0&_2:>P M9F#F2`;6?I[RQ.RD2H3ZE!I2[T,3IIH%.+!E;7IAP>1ME02.97E%U,K!6\!4ORZF+EA@JV3./I[7RJCV?PWL M?Q+YN?+JF]Y/32AEH,-4@I+$H,A&!#$<240D69##B6QH2AL+; M$]NE0_Q;#>\FWI6N^O[A"XR'QR-HU!N-A&F?UVPRN!"",2!V%^/0)]AZ#&&8 MI,EK]F'.J!/^"Q8]P@`F;8J*,:WE,)O>J,"D0]X9AB'H=BT%+7B*;9"("^JC M83D(JU4#-=D\B9-UH!9MJH<8X:YV6Y9BS6`,X!Y74PG\NDTHM;X/WK90C@J7 M$.VA/TA<=\6;L<8[<6=[U)I]_$.@\XB6H$N?2AEL=.O)A<_M9BR301U.$Y\" MSNR#KJ0QH^V$:O]W('5(GQ+5$Q:`P)M@0]7YKY.U^9=Y4Q-C@^\XAM49D#J; M29WT\T83G'.UVZ36[1FUT[!`&"7BNC+20MZ&<3"37E;GLD(.)%8N_[J/NCIC M-FT>M>^CWX]=13K`B\IO+X8NREW+X1&B"F\A.Y/#1T"@WFAW-'0X=Y@YG M#^>.AXYSQ[/'[V[M*NT"YN5W97SFP,&3ECUIC#9:M,]5B[ MJ8["9OL5RQ7WE&7*/54P#X8&N<'L8`XGC4$6#:4%*5N26T%[+LWA"`Y%Z"@T MZ'C&"`TSS[`R7VQUNB2YM2A+0L"LPXVN#C8/\JOJ7$.L",157F\=8=1WE+*9 M$&OJ4F.*SQ^(A7L1@170LP)("6E!$8X()P2=<`$T*'1O0HHU]2(R*Z-G99"2 MT[(B'Y%/R#H9_OFC7A/7&M/AJLJ=JLKW1^;+Y>$1*/?BA_L:62!;VM0L69XA M9\M/`--<8XRGV%*%S")HX&H85M=&T]+E+(Q%?.8`%?"HD-]L&Z`&/$.VW=1NS[A-Q?P' MU`>>R]1ESW7JNL=KH2P>5.4]&J%X^FNPUYC'7:!^/I6X\5FE?@4VIN3VM+;`?5?1]_/$BZ8>?(H#[_Y">J)X`B/IX"1S( M_.2Y`S]:0OV`5V4]ZE%I#WF8AGJN?N'-B8J]*THLP?[92%4YJ!B&2#`[78>? MS(@/>MX1I4<$`B80HA'_A><+?%H_;?H//J^?-Q$P+E+[;/O($=<(I=]LVF7; M26+]2#^^68^YH?VM$PQFFJ!IG7F3`S@4G9J7`@,^X%/,JO$-^.'BFRV3\^HH M/K&]JA^!+U!V(+DLHF5"I!%?LB?0:C@E0%S]$\"^0FY>J_P72!2_8UMK^]8= MO.&-F^I.#`[?!G+;#A,H@KE9HA1O@]\KK+IJO MCX>^9=E8OY&9]$WZKX6FV.GZ:>8>^T5HKKY.7P^(^@C=3/?2_?1VW5#]$/,# MW4_-X_7CC(6D@A*9Q.R\C4D6&AP\0Q5XL8F1QGC1;#(:=%C$+G+)L-=A-NBL M^KX`0>FM?9PY*=DV8P!3CL!A@6(HIK2'B\0>A9K8 M/=J%!+756+/(P^6&ID4[[*)R8&E,:A?3A:HN+.)6C1D<#W0RXE9>+$&I%FZ6 MTI("WHA%>U\Y.35]JF]--`X`T;5^X=;&H^N/G?WS=^F*C=E:D8E4.ZY3)&/V MC>Y0_E\//Z_\-4.G/SQD7U_4Q50].Z&>/9#!5GC+CBE;>7Y M/:R'%0(4'&07CEGU@ILDK'V".>"W86R,\JCI,694HNKHJ)X)IL>YJF.",A47 MH$Q[:CK!*%$-CL/+DN-3P;$IM^P6:2$*;43WK.U:_9UUWMAHA7I\\^4U8N9D M(%E:^&Q+BQ1[9N"7-[_YDA.E6[<]./.S@5/H\\`=\^;V/BJTY(C,"MVSFT!0 M\B6`^S?J;A)@?MH&=6&1MY4-/)FWG"$_(B?).^0,.4\:=!80#)(LRAHQ'F'8 M)WO#/\($+_$^RHW9_9B?]9EUF,>ED#`QK++!7<$&37::,W%^R'DX*XKQ>6Z, MN\5A7"AUHZS9QYF:A](&9MF\D,5RU>1#DK2!IU"B6:LE1`N%)(I"MWBP?:RO M;7M/<_M6I[BAT+_P68:(%8NHI,+XY,:7UJ\MKAW=OJ7R_:&<(:/.P8JO[J$/ MX+UJ1O+(/27F=M#2)O.XY7QB,C&3^'?"8+6C"=$A2$/F:[;)R&1T4KPCFMZ! M0ET`?S_7?$YIO`",OPHEW_<#_P6P\QQ]3J'@B;(AY!1,*!X4G`0N),UY(I^G M20N!<:A)X`C%Q]#G`DRHU]_:\R4!B/U(?"S^3AR+%Y653#-@0LTS8DXSM$"=V8RC$"2]!F]U":*`M M`8)V$12T6;%MM]M6;&A_M-JB;2E];+?=(J&M1+5=I2PK4152M$7I`S6E4@7= MM@MH?Y15?P#22HG=,[:#J%2$^J<39WSFG&LG]WSG?N<[Y.V&-JK?(GY`N5$, M357:/5$NP^,\&KX#;\,+CG>AD:P9RTE(H-#O"`38?"X4%X,- MKEXETZTI4#0BR8(UN3%_Z9(OF$WV1_HZ[&U?'.V?)I\HJF9??N\SM=,3RR?3 M;9FBK8P7)B/YKQ(G6S-'_3W7!JBK#CA1;U5&3!5O]&WDB9*OQ!-NAE551E6' MVM:W;6?V,Z>8,\QY9BY\.7PM?#OL%WBA@S#C7#S&GX_K\5A'?SPX),0#L>`Y MS%<2#<5`>/:(O"U%@T*GLZF^6?R+'#/YRM%C,2$G%`(-\=5 M):`]EF%2DJHJ*L.%H1(4+`3(]IBDTXKL&6WX*%UZ4R*D<_A>A9-57>E5WE1( M!1Y_/J8[5'-M9GFR>&-Y4B[..'3CS"QP2BA&2`LE@8&;4Q#"7TH8=NB,)(%< MX,'8`GO&<3*+N^!5((S^57[7*>%KG&]P%>[OSJNUN?Q]K2\2U5/D69L(&FR: MJSV+=ZIY?UK&MDU:Y:4_$;LJAPK]49>]LE?J%.PU!S7\-I9P@-(XDX]+DA0( MJ9JIQ>5N-9M(=5E%MM\]H(VP(]HX.^F>R.Q3CV:/J[.IX]EO11%*MBKJ.0RUN7%^?%XDS9FE1FBMH5S9**9>V&"+IG!%*C%!:,#%2G' MO6&Y=A!O99X*17G*M@E)\W<9M9?P+">Q:W6T,T"Z7[C+PX#JC:C[I?=(WT361G/).^8Z99]0SVH*Z MH`D!T0P&JY)NZ*))T@'#T$U3I$G:SML`AV&*>5NW+2:?KTHD21N!0-!\V7K- M(JR49(JF#2N9E\6?B(28DAB+T8.,&##(O&72MI=#/C5*W,64M.Y.4TK(<[RR?34\* M;*G$9*GTI"+,EDK@XM,"NT@M,NP\`['FO<2PT*LHB,PW>PTT;>>%'T;N`6S` M(`R)&_+.43+0CQR$P1MJ]/-H;FQ#^UZC]J&>Z"105=F?W&OW#>!M"35K7,6] MGHA<"Z3MD#?B'Y!7ZQ_-Y6JG+=;>D3B>PB?Z%,"1?D6^%;\KWP/=E+4;Y M'\^WZ3T0S[!!0DYTD\%85X@FW..]?)YQPOG\@P7)$$KB9'\N5+`NEZ[/-X;; MHE6VX%*<;KXPO`)&TP=G"-C*N3>`@6/3$(["%8?:G=2'&R*:"3:I>X6V'G5X M>.Q0.3:V#O0-4T&_G8[D6F1&H-XRXWU5^`KG*P[@_F0N4OO=^-$O[?P,_MO% M-8/)C"^\U?[F`UZS<=!@E/;:%/YL+",VB:^SNO2'?_QH]Y#K*N07A#?Y2-C2\IZ?3FNZ5-=YNM?[-P?Q-8FG+W M0=>[,P/%?0=*WIE+&EF;S:9GOS"/FIYFW>8*.`&")V"$<$,;D#B%W[W\G62> M)^[7NM]9.YTO&K57\F216/<];.27+E)F[F>UMV!G""HGC[Z,?HBNX"2>)DSB M`CE%WG2]2+'43ZD:_2E&9RZP:]D%]S0WP+WAL3W_]+[A_<"7]'W`3_/_\G]= MH(7GQ,.2(!T."(%MP>D0'3H=MN#Q^A"/D%\0I0`*PB"&%!4A#44@'H6Z MUPTS#MHFT97L3J5[,EFKM\_.Y1__Q_\?EPN]`/U`DV@_>JY>AU4ZZFE$5T-T(_H8^D0C^FGT5+U>_WO]6GVQOE"_7/]U M_5+]8OU7]5_6+]3?KI__CQ3^MXM\[/_(HKVM;R'A-*R`X@);;-DT6*:#K,L- M'@58J6D3@,N&EDW"BNTMVP7VYUHV#?;W5V_9/+)V?7I\_X$]1S)K#CX]]7@' MI&$+VHQ&T%JT'J71.*3I`-J#CD!B]J!]Z!GT-*3F\"-79=`:=!#6//I[_I<5 MK:P4T"[8VS'(&`&("F@("O1]]U7PX14<]G^#?7[7O\5O\Y51D`/,/VSHG06C M_[_]%\Y^B[4/R.6$J0<(,`#L\+C)#0UE;F1S=')E86T-96YD;V)J#34@,"!O M8FH\/"]3=&5M5B`Q,S,O1F]N=$YA;64O05!.1D1**U1I;65S+4)O;&0O1F]N M=$9I;&4R(#0@,"!2+T9L86=S(#(V,C$W."]$97-C96YT("TR-3`O1F]N=$)" M;WA;+3$V."`M,C$X(#$P,#`@.3,U72]!&`G`F51E!"#KB+(1&Y0(0[QL$[DL`E M$A-K)@-(((,B](!"_<4IE-(B.HK-@I&Y`$)JL5BE(V.'0ID"K<#HB$QM!W]: MZFV?W2`5]YWW>_]_OO?[]O8@``Q!-Q0$&EKC[1N/7'D&F'<4$+L:.COTGU=6 M3J;'<4#-7]R^I%5N_KJ5_"?$XB5+ER^^'"_8#V11#L423?'&*T^<_PB(GF9, M>8**(:,&]0">+,JC$ZT=R]3.P3,I3Z1\=6E;0_S2F"\7L%XUY96M\67MFI<>`R'KV*GZ>F`;4N_9?U9&<7H7AMENG(*BI&/+FQEYBZ< MPX^0#1\NB*F4>W$"YW$?%N`H:O":N!=)W(_):!45&"T^1#E"^`4.,V(YVNA; MA9_!RZ@#UMO4E>,UI/`E/"A`!2+,LA$O6D?Q2WR"+ZR=UJ>X$VOI<=+Z"*4\ M@8V0R$41<[:@7?AEA[4.4UEO*P[@G+C=FHK;,!%3$,02)-"*1_`D;6_A)$Z) M?.[&CS+6J<)\;,`S>`$F?B\*Q>-BN^JQ$E8+YK&#%L8]S=V M9$0K5G(G6_$.WB><9U6?*!PRD_.N(,QF_X^Q MTRUXCC-\!:\3?H<_8588K`;7.U6FMMGJLP]8'/!$7AG+^M83[ MT(%E6(^?L-^GL1]OXS3/ZG-\(]PB2V2SAUYQ5ER6D,/E6&9[3VE3DDJ/"G6; M>M8UU;4NO3M]T5IB/6>];WW-W4NX.7L?[B),8HU*U&$NHFCDK!]V[L>+Z,%> M]'%V)W$&9_$-TF(4]WF7F"X6B!7BU^*H."Z^DE)FR4+6'"O7R1V$?GED&].=Z97I0U:M]8*UQ^IG M-UYV8Y]I-69RMW6HYPDNQ@IGUDG[+K&?-_`F83^[.HA#?$M/X.^XRCOW7\[! MX\PAAY,H$Y/%%#&5?L!U[R,G(S) M&9T9NS+><#_L?MU]!OLXX]]P3]]]&K!%2%2E0$C*J8KI9'#/58J.ZVF_+1IR*^'<4,5.GJNIF'U./ M.6[ZS9X!>B[^GF=@P#-PPU-DZ5,PQ5^BAPS=_&/0T%-B05V$_*:@$=7-*PX_ MR^&W.+Q&WNME@![*201U4\3TD%G5F4B&8D&FZPMP8(/\);P8G,1@.[&)&?&N M1`Z)[1$RD`E@4L[GX@Q%3B4=-&;-K#!]O9AM!,WO%I9S_ MB]]RH8W?,9JRJ"K>E*SB:#94#X@Q6XIOI%0[5V=:N38:,<7:Z$`33N\#NV@R M0K8FUJ*;'F.ZD4BVQ#ASS(GLRPWDAHQX,&HB'-DW,C#2$?PE?3FK[O%R*'W^ M:?YI-KW'F[-J@'[\Q(#^P_[!CM_1OY'6SKDQ%V%7,F:R35-O<(H8['62O31- M0K)A$MWX1`5WV6QZ9L2267(7X:30EK;0K!@CY^892'%M+LLZ]#G)F8U*OTA,\<+7(H30T):.EW,[<2#/7^HC7#$3S;K!- MT>C=S#/>SJ,Z>9)19FBYGJ'%R<`$W]"II*26(RH.1^HB9GS9/XY,Z4"6N+V^/5Z^-/P_E($T M&>V=="R]QWW0UMST5+B.P2O)R%>QD%A.?@UIF'2=G`Q5I0_I2^Z%Z*/O*-<\ M&,0[[3CU`K+5QY!-?H*3YU5X28O\AUT-.8H>T MT>96VD`B8\`_B#8-64@Q$!JXC8>3$WLQO&8289` M.TY=.W&FF+HF8\_$3N((V?'(3IJTM=NQQW8GF;9).G%2)Z4DGI3D#SNT=8SH MNQ.QFQG^Z/1&VK=ZOW?O_7;?[MN5=K]VGQ9E0??T/LW^?:#[ZI1?X*I3^.9K M0<[M*>=2>"S9Y@'Q9++M):XZ%P^C$@6&$>U!)80D=Z&8+'=BGRQW8)^,/Y84 M2N"UP63D,(B!9&0:IF,+\LK@(\G@-&A7)MNZN.HL'%ST&4`Q1I(KDI$#`+N2 MGJMC1%X#/YBAB,),F%I=>37&DF>,`K#\\?:>;<,#S%&<[5YN=L$!*+*[CU MWZ,?I-?3(;J,]M$.NI@NI`MH(Z-G6":'R694#,,H&04#ZY8QIA:NBVZI8!F5 MK"24"JE5R'V6D%HB4\\(S!"PM*3S(H'WY@U%S5%]1!>NBRW1="^V[J6>@L1! MJ)6)$P7MB8#462AH;TJ428?S6?PI_GL\=A;/2*(=?O/XTWBKK.=C[>WFID3S MVHTI/!/O3P'0#W`&SF"0DLVDDR&8",2V;797,ID9+XK&IDA+9A/*B4=EDE/)*)C#A&>8^ M>#4V)0BRE2J!?3)OGRHA.RJ0'06#8!()2B93@2`83`4#,BS<@ST9N#4#M\IP MQSW8FX&/9.`C`"\YQ__'TU?SO]F=ZC@T/"'=EKKM\3[X=B=^,@07PCV;BHJF MA@\M7J,`XQ(\(L6*2['B4JP1<42. M)8TMWO]`S>`2SP^W;^\:'.R"30#_IQ#U/-4$%9]&M:<)W$@I8;N+^4A!-Y)( M12D:29*P9BGI1HPL3-;G?%VKV>U>?:NR9;YR-3M7V<+.5Z)HY7PE>PL:OR^H MXW5.^/+44.KKVU33[==2Y`=WBN4]UY4^0&RE-B,=BHOYV1H%J6&R#0I%MH;4 M:0P&D\FJ.,DTZ"QZ0PJK3_%/9@*US-]:'>^+S:!H5!\.8YT^#`)=8B_Y?7I# M>MZ>\])PV1\IW?==>OC/YTENS`]N8G?L_./Z/I M]P_P%2_C`BC;,I]RX%,/?(SH?K$HB\!:EE;"AU1K::V2U2D-><#)V*`^J;7D MYLF<6C9D.-V:_S8G4QBQ,B74B0@:*-'.\E"YCG42SE">2:\CZEQSV8.X/Q`7YC,OU%^F7@]E[Z&IZ# M?ZX&X.:XJ,`DP9`$J=00),,>I-6YP.R72JQT&RYH+,;<"_R.16;SNV:WF1?) MM5[W;E,'2H]+[FGHW`92U^AJ@G$S_!:ZC-3((1HHEUJM`>:,B[!D:\[S.YY9 M)'V7L-^G^(:846G'A36U@E!3[3-+HD80:F6?BH6/"`'R1J*(:$8DN49/$)@@ MX;!!)*%>9'<.NQ"/7YSZ!82P2`3-L$RCE1@2]G2+U_T$^SN8D2"VX\N]Z8J' MJ#C,M6+EJ&4V%RLA\O+H[C?0/82![5SVCFC@M(JC;G:8J/"S1AA M[V"S1:7&:A5)(BMIMN@L9K4*4TJC*^0J6*:8UJC*4 MI?QH^NWTX][V[/0-:;\0Z-C"EWB,?`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`N\#=XQ+H$KABM+,I*;5S)) MK\0',[*0TBFFB11:[=Y4IJVW]>M_LH/3=F"W*\%,%I9Z4S:95$CX*=->]H7O MP0?*\4?BDW$BGF^A="\S@1.OY-MSIU""8,X.59$SEIAJ1PE56&ZH4KOH+1;K M])!%%@W#LL5XNEF260X#AII0FUE]$&`R/@C27&80`*EIT')&>'P7'JC>DO-0 ML:5!RAL(M=LA2&]>3@M]Y$TCKBIL>/_'^MP_4UN*3W8\^]<7]9?&-)0^_/+X-F/C]1C0QMO?#53G\>JST[*_*9@EV`G<<4CT#L0G<_HJJ0)95QARZ"/%A'1;(>G3"(@NN1+AI MJ+C(@BH7@:!1,$!;3#3A]@J*I'JCG@+F3L"&$7T%C(XW%<`LQQG7FE=H]\LJ M@H1Y&6A0A7H.D^,-%TL0ZZ[20MYE^'-ZY[9S?S"O@]@?QW;VK5:[UXV?-%\] M=NBU*=#AM-_?&4^8^<<&GC/'S;=A\#FRU%BA+E^XX?=O@"0P?GNND4^W0DW2 MD-,SY;8I'KQ$3I`3D?BDEO1+/*O)/C_NRG(8]54*Z^41<<=;F#5B)4);`"ZU]'S[[MS=? M,O^ZJ-7X@&L+ M+3P=X3UA$,X(A(3QFI:T23RIR8&G61[C`)<)"`&:",>2%*>D7$123=C\-.E1 M#R:RFB=+!OS-@BAJ.@F%J.M$F!NF>EW#F-JOXNH$[CIL^&*ZC4`PC70#YLVA MZ>GIDB6V#M2A:U6F6FWD&:0]JX#K4?3&$*A>,XQZWYBB=%J8I>:7LT"V2*+8 MTNZUIJAJT8R0`%OIZMQD*SOSD:_^TKR:"8+YVWM"+2ULSZ/F\;[7S[RUK#AT MZV5\M6(!7-]%JN;YW?V"9A:^,&*J(WVF?4'HWH/FSR!"*_,AGFO@)(GM+Z_Z M3(Q+,*2R3V.,2;RLR7681$Q,0HRS_&023\IDF/LWU=OBZG>=<1$N!$^=A3>K MQ)M#?1`>"J!C2(R_@?N/X_++A;L)OG0TY=SF)P^(!Y16>!-LOIG47# MM6.*NV,',5(']'AO5)\%5*YT4(J5MUH_OF!_'OI4#FO!)LO\91QHI/PP+[Z8 M"$N\H,FW&Y6SW%HWJIPBAPD?I)!JRK;DH%FE*.<:.0*W'6KS#!C(M]I:+=^Z.32$1`3W5.9BW;T0&)2*%T2N(=,"<%!%-M:H MVJB6=7MU):-Z-61>661>:61>S?]M7I]E7?,^`1E$$:&[%!BF0DP5LWVP03#6B5J M-`X84RNWX8&1PRO=-K8DA@*)MR$WZ:$2!%.L=./KH;45*UU=E=K4YOFU?=VP MKVMM0R>IJF3G!K,"]LZ,/ZIL[("1I*F\`_S`7+6Q#)5G^3[^'\H: M`I-)(#OS9RP8&9F6>!]LW3;"YD MF,LYZPL0*:FOOKQ/+$$^+YZ'GQ&O]!]`/QDGXI?4.=UD/Y.:5H,9W/VDC= M+_AU1<@+O7R7X'3HCG007@BF[;]H!VE=UWV"P0M1AJ:;?48ZBAM1.(=7C+0N M1'F&)IV8*\@13CY$XG(.^P_=90/;Q'F'\?>]#]_YSG;.=N*S[\YV[NP[VW%B MYP,2H$XY"(1`-FBGN,!4-Q3:%;32*%$)=)"6=D6H:"O;$"K3*B%:8!14P:"A MH2ML*P18^%*EM%M)T;H)&$*V-JE1UXWXLO?.#D%=%RFGNXL5)<_[^_^?Y\&K MQ7J9%H,UZ&>$B^>#"3G)+ZJ6Z^55,BZ;FZDIZ:I-6(@T-2)$BID,6C7]YZRP M:D+1FD[[D7Y%/F-=RJ_2?HKF^`S!);ESZ`X549CK->L-BJZY;\C;W&(%,.N) MLC^89V.0*HFO#F3:^K&.3>VG-_UI<1OF7]W[E+$9WMBV*E=\/9N)U1A;%J*] M=5IE%KZ";^R9A_BQ+7C.>'Q?[Y4Y"4&3F3FKC1\7BSL7L1$5KPJ[VU/P\$/& MZWVMC%K>\[8[Z+Q4M,G6W9;1'V%G;5*`Y:4$.YMMEQZ3GI%&["QC9UBVUB.* M$F.W)SRA4#`D,CB@G)3H8!%H(,+CE:)/"D95LHK6)3E8%7?$W;ZX$(V'Z;@: MQ]$O"$JD$!:%!.6YB^F3:U]BTJTU/)Y+H_<,I]O30L7!:0Q7Q(Y M4_X`27%)`M4"$JE+FZT@!QY0U@Z_.8PP`MU6-9#YESK:M\#=\#H]ILVKU_$7:-;EM?GD13W3WW^H@G)JX=:I(= MJI4Y)N^0AY!VJ-&!/?K\S_QP16!MX`9[UW6WZI9D8\UB%0CX`ZR?#A`T\'+( M$SP,%@)BF/;;91GW^7E&8-UQ!UO+\YZX-:F.2"`<%VH)>[PZ;JD349`Z^7RF MF$<"Y3-FK\I/A0@S7$R8NB`T32K1=RO"CR.3')$QD2L#%TM!I`MTHQ`_1=Y] M12"21*J;.Q=VXU6-D"AQ+\79)$LFN55[H1;GT_3?87[,8VR6:YA<*FN:7 M^RI7N!_:+7-K!$)`K=*@L$`HJD1"6Z,`ZZ!=H\ M=(OE=W!JB;\,!Z%JG!J$T)@X/C1Y MY^II6`FK3E\9/6-\:7QQY@_87KC:N`3K8"=>%$0D[&?AC$//H3"A)>Y94B+&IK*[(HE87 M\2BAF!>GY%0HQ712BRB-QZT`']-H5Q$32DG^$3\?FXJ6/N< M,V-F?QK%@8*[E#:3Y5P0"@19)\`<*M38H"L+L0"Z."4F"X"`9Z>3PIKH!357+D,MPF:0Y9Z!/];R[?-#;8H MW$\?W35Q9,.<><]A$B1@I7'UMOQ,8-'FXEEB5[L62!;ODEA\\<6)I>RBE_"- M/UQ@UT8.?/PA;OSD^8S=FK-68Q>YVV(K#OZBIU7_07;$]1'WD6\D>D4=I751E"6>3B'`/H`*4&!01X\Z'Y$Q/H*1K/0DV17V M[O7^SGO-.^DE3?).U+!=<9.ZFD2Y*A9NFLJAB1(&+E_V"V#N5X6Y!>YS5!,% MOR5F1HD!GQ938]$8;BOS&/T6'F-3//KX:2(!RJ^9:2C+K>G_,$GZS%F-*%$T MR6FHF8#^#Y_LNQ-8>Z#AJ3Z]:=8(3#N7>_C=03P\:@\9_!LTTG M.FLJ561"OR<=RY[^+4R#AUE#I/Q6D9-GY^P M\2JIV7P(>,)/(>JAQ3SL-?$V';F,^#3;C;ROJM)&E0QZRIFQY[O?_L72EY?' MC*W]<^;U8"V_Z?_BPA%X,+:TU3AI^/N0+5_`AK6V4\?G10(I@RJN9=NWXAN? M;;-K==F;O]PO%/]=7VM3L7[26%_R8PQD)V_A!<1Z,VB!:5US1UY@-K,[V!V. MOT=OJ50GO9+)JAC+4.IKS&O.[>H8,ZI2S6;-<,Y\45_9L*X!:]A7FQ+--V'A M1?TQWP]\F&^?YHVK3H8@PJD6+TZD4G9]ACAS"*[3*X#8[.0858F+5$M`%-"[ M04D,B2M0=6G2*UI$KC[YC^1D$D_.;EZA#,$M[P.NGL.XV;/2ET=S`X6;?FXT MA_3][D#!/^X7"N.%M.5-J*YQZ$$H+6V4H3FA-9\S^\G]F]X^ZSAF5->1GJA+ MR0)[`AT%68P.9TNS@Z:GM)2FNHP7 M#0EJ+^;Q63,RV9%^ MX^BR]/*KA]N'75J0KJEK:+SQ;-=`??W3[[VS<,&7I[NO540#1%TKO`7?W/&] MG5MZGEJ2?F)]8].3&WYU=6%4-KXS_.::%&T$SQ8+?^L.TB+F)'X5$,^#.N&W1@6AF$,*\;V"!-NYTV;PH"S.F@`V@NCF.=<`C2NHNB$YZPN]N]UWW43;C1J^.@ MDS^%V8$_/3X^GD/C,3Y^V[($L\K,G@U+XP`^S\!"'BV?'/KB"OF&>J]L2I2$ M#X0F2YTXL8UMB/8<[T/)_\@K>M_AS>%&LM/8OW_-O3MF[%>9^=L(L/J`R:Z$ M,L#;5I;4P,_UQ[-"EY@+_I?NDZ MH6D/0:M)$VQBI1(2E`H8^0.4"JV=;SC73DJ+AJU[S_61K2.?[_?\?I_OMN`) M]D1P3KH2N!MB9$IFNZ@N=I@:9K>*$])$8")X+G`N:"7Q!27:_7M(E&FW[]%# M3"0BR8EHQ&\W&A79[4*8R;4QBA+F[;8,[]LUM81;%M.]WXZ'?3?_C]_M?QX7U]C-+*L80- MOT?V(H0:]<&]PEX1^X5I849X)_A.Z(/@!Z&[[KL>AG$S'L$M>!+NA,=,,PQ% M()M!ZQ!#N;.\:]3%L!XG!*705Z7ZPO),765$(%#HV'N+=,1W)\\R$M\MP=1&IO%5J@ M`=R=E:*U8B3)B?.K>8>.>[XR8 MHF2OF>6_4OO)7I?A08XQ(%'"*,P)"S=I(Z6+>7"MM*3PH0T+1R07D`O MP"G'*6X.S<$9VWG'*]P9^8PRC^;ABN,*=TF^I+PMOZVT-U5T(I>1$B@14WG( MY]6L)9W)9E,6"]-!/N5R;+&S5"J`A*9HE^2\*BB2?#;ED+@$&Y5B4U*W5$Z4 MZAE9S*#"PO+T1::@ALE8?US,9<-Y-:CJ0EI2V6S&)8H2F\LER2B4"@5=6+I4 M4&EC.9_+"JS%S$@I62SE4T1MDL5H2Z$LQP@EX(*:RS)K_'Y17H"1^3`20;P" M:]%AQ,`;=4L8E0^7<5FHK%F`/UV,[-M)NN#&):+T6$/D&[KB_,;A+P[I!:+: MU/PAU9V?(OS##VG="FF]Q>J_:7IB$?[?C2*FJ%(DKMFK=+7YX4@KNDV./^@3 M=8Z!,D3C!HBR@,D<+-?$',M"XL8NJ2O:J-@: MF_=#;^H3NIA$2I(XN\'03)PM#0FZ2O\K(M-"*;W1="HLK'[/&_$^MO5K4/_S M\].[\=YM4M)C<;W_MZ*+S4BC<'MS=G1"^RT<[7O\T<;I)X9WOO>ODC?2&5JO MQ61FY,?P35CW_H1140R,+=,6]XC:=1!KLL^5=3!$7\S'G]..-:[O4*UR`HMR M^/M0U-X=#*E\QL6:9-*_LD3/GQ(]$RB)7JZO2]$5>E@(%QL M1]L0_*I7?>1SVGMC,XUCLX/:TNR^37A!/QMBVA8/:Q5X-Z`P&;N^>8;VTG&M MH$U.]U"R3`_.P!?@Z+5GC*U>-Z]=Q;O)OCG0<#U&O1Z#0^WTS9C]4)2B[8`X MN\M)"A1%SSD<2."<'T:^=!G\J%F*JF-*)W3^5\\4ZR]I!V%9;(VG8T6&^_O[9-7QML M'+@XLK3=CN9H2G!P'T86X,2K3Z\L35;F5I9>71DBI54Z2$,I`DO:IDL]/C9> MO0`7M*ODY$5-GUVA/4:9RO5TLW5MC^ZG^2IQC._I3=?5@LB-U/H53"QC5+8-\7!IJ'S`. MU1WK[ MH@FK'R@LVQ2SXE+`3N2D>HU!Y(WY@R2JNA4N"/&$P8H4`&1WF/KH('+&/<'[ M^`U-!%\)L,\]UTRPD^.KAUE'\5AWE]R*4\UB[B6L1;B[">8$PELTUM6MVY5, MQUM#"?"&9S8DUOKA=ZHP+RF=J`^&N@^-X$34S+[6\:+AJVH]X0J_?KJ?N6,%LA9,VB-)P MP[L)M<'QJ%FFHA')[&4-*-++4M)N)QLHZ^,BUF5EP33T" M!\>3%$]Z1,!1&'Z<>NK)[3^9MTOSC=]9TNDJ^^5(WS?O M35B?85_1GZ(OT1<=G M]!<>/&V$F=TX:A@E5C.K[>.&K<0X,VXWAO2L`RA:W!@,)6ZKHEIY!T9KA8J$S1BN2IX$",J+,J-BZW MC[`@P.*F1,3D@PM!>ZPB8N8;1(5^@%()!Z#=(/4RIU8^M>.I"3_#UMF40I(" M.OZ;F"RD2;*!][5N?.'(WOO[8WDN5]RZ_Q=7@.Z/4>SHCCM\.3DFI^W,^[]\ MYLH<:0F]9>X3US\\!YIJV"0@-C/:,>@1>>12:C6J0];$ M'HE-Q)Z/'8Z\'GLK\MO8!Y&IV'O9RY%+L;]F35AD?A@5],:/-0L)SKB;]O#L M0C?GV>-K2"KB1I\2YJ7N:G@CH4H"C?;;0;=1,OX-EP[\BA#RMO;AJ9Z-K^U.3/ ML&,\$P0=[3$4\S&DD]2:T-6YK6VSYSI3`/6A9A_&M^G%R&_VH99MM M&S-KNFYN6**_5S]"G]&\;YG6?&'XS*QOUQL(UH$9"-1`8#HV1V$`FX?I..Z' M;BN^1_>2#M5U-AC=#A@,W=0Y`A`*>[W8)4J!WNNIL7?8DKLZ4^?O3%U?*[97(B6@<'.9E$5U84X/*#1H35A(F*G.?@?P$5CUJFG`(_AEIZJHZ\P MV^G7B_P)G#0Z$IL M:L8._>&-+Z?7KB(?_1O@3IX%@=Y5K8ON20SV0L\,(0A&02Z+R$.E3(8`>D,C M$89@B%@1X<1/`[XB%_Q4P'Q:T6IWT)..I!%XM3F/&]?IQ""!>?@0")U`-26# MR>V+XW$(X$EP$Y'BBN85IJX-YZAZA80)9F:&KFD?W)Z#.N-0,J(:$=.TD$ZF MZII6F]\84&S"#9*,4(LNH='RX<.119<&)V2_N\E-FT3_?)?YQK?M.RK_YK3= MZ]"=Y7UK_C*WS9<2HD[&W1?JG"E7MF\H&C@XLQJDM=J%O0OUS(KT($N1`>1\ M:45O5T]YHNM'Y4,NK3:DS1C*SG*N/(H]F#UH.^@P=%JI6$\TXM381;\+%>=3 MG2T&^(R%EQKZ82M#ER9[O.$%X5-A+#QO07+`R3?B:$?.-#`@VN?W[Q8/B*BH M�YI$VV\D.Q]F[);CT!+I1,A9.+YU!VV;[;?L"NL2L>,308GZH,ST`RP6MJ MN@(YI1!)X51Q"B(W=GEX3&%4O%*W\-I@J[^<8N$*C)::`\#(!^,=O!23M=3< M5?D"LY-@9VOP2OZ:)_/*LZ;FP478GY1[1LWFMSPZB9U]9_S@^3M3/PTN\MM7 M.LBX+*UZZU#OK_J9)5;RB(6@WSG0V.F^>VXL"\#R9ZK[?_W*Z61?%QEC0]T; MK@4+*S:L#%K'[M)7_UO:=&<9MBB`H<"D+99:4>FYDFT=^Z.ZOAQ,]X^^B?9"O%LC7?T%OEI'C M)7NW'7S+`@/K9%&GGHI[950H@*W&$60E#U##45U55;K71;4#%`%;,W,U`=V. MZ'4C5U]8%B7=62/3$-W1.((6$X/WOM3&)^97%PRT="[[P9[4DNH\SMBV%CN= M36-HH"&H]^"5YWK\A5T]FZOWCY8(CB/S:\'DBBWKZ:IU?9;D:AX&YQXU01R- M,.,,ET2!-!=)+L@'!)YW\-1"EG/LX7@O9=9P0?TDBG!X,$!(:N+DC9-:RB18>>R!K,,M&IB5RM)O3HYD55:>VM:-=_7J#)M*;P2>=C6&-R6O*N4E< M7VG9F->K>P)PRA'LIG8#DD4NE,;F!@;Y,>8)YB#S5>!_`5S#B[SH:^4SOB'; MD'P?/RK_G"%\?G_.8O,+C$WPE_R++;Z$C4G(C&Q+)&3![X,)5?34*&-&/"Z. MTR&M84SDLAF)8!+P.^869%1J<8](CTFG)4S*9Q3N&6V)>)8W?GP:BJ%"H'Q. M\>C//X=9G)H>/J-:,PM;7-R!U$J=TNZNSLS2M;?P/:ZGG!$G58!W%<+;,IGZ M'G(05#JHM#RUY)F`&;"0<)!`F=I+H"1J^*P9:9>;K1R][+Z>**[#`.-AFO/@ MQ?6[?M]V\NG=_=6R0'.$H?JGI*>WZN/PEL785_-$%.4<+H=9:YA]\ZJ+)UD2 MXSB\[UCKE1-;<2>'`M)DM)+@V>K3W="./!#[H,JG1Q#V_W27?6P3YQW'[[D7 MGWU^._OL^'R^V'>VSV?';XG/+[%CQT?B."\D(927*(!!#/K""BJ96#8VL57: M5KK^,1A3::%2"U)'NZ*MHFL+[(\J6J/"I*P"J>P%L6[38.O41?UCE#]&8_;< MV0FPEW^>/#G'4N[[?)_O]_-#QE3!C6"#".\1PAV"TW(=+YEYRU&G`\=P^,>> M#LH+??2VPYG&<,U!K.X@W3Y0@(D'K5-XT"[Y0F;%+%V-`;.K8A.]A]\CL?+V M)L^;BANPJP/>+H-!#)*<-3'`_B)82?%,+A$A\50H4JWR>$ M1DO\A!"R",04?*5C]L%17T$='1E4"_EDV.2%\"P:JVK^4)ZS1'UBHJ.J/#)^3K.R*-I0E=E M75K/G+G;0&6M4B?H)7I)9PQ/&YC;C->:P1PIT&CT=&OPH(?Z M`R0'O=,)M!_0(/\K?5HS&OF?CU:>B)-<5$ZZW;81^2V"0'<='7^\(KC'"CMV MG=4R+&F]$FY#MG&L))\F/]'`6V4@1UDNRD8@ MX'&R-W:_#!JS#]N["K13^3]EL'H:0!HN6I@^$V.+G=A.8MNRDQMKO7M+M>:F MT9*ZN:\2S*M#S;7@!F_*;8,NYN!-#EDR`IRJ/@;.; M9Z.>W/*5D1Z4ATIB2/;>GR$CO0$[@46\R#$U\8'IE@D]3I_H.$6?[?B<(CH0 M%^[Q;*(VTD3)R"I>E'0J1K/77?.:"8C&[_KL-;L9F#4Z]G'MP<19U.$8LK$N M1P+Q6"4+L$<0#^:.`(<)[A@2[FP(&P$=.%QHRAE!7`:XZ*6JFUGOS@8'+8NX M76@HB.00#5"<.O.@H4)V^=('`/_B\GSS#I@I[3Y]9/_!D\;BAZ_]%&3*FH=,.A.>0RS010OJ3-Z4%X][3TAO2#^6;\J? MRT9*(N0Q"3L3!D-A$#32@U9>N1Y.#?*9CT.LX-!+TFA]-:`-1,AL,#0N^GBY>;O["Y>YL7'TT90RW& MZ('Z?@*9FX:T=E7=1,6Y>"&./9_X2>IB:C'U>_23U)T$.9$`O49ID!<_#OKT M"XH9)2OK<6$^@Z?;)W6)$9<1PVDO2RG=)$O2_5UF4;`99"G-J3[@TV'-6GLE M"9*:[718TVRG:?M?PCH4L$+0;5VC\33).*&0]K@U@IC3<#$Y#'[`N&P).H)8 M4A14G*'\F@N!/H[%5T`NG'_@_FJL[(1I"H7V`W>[>?7;"X1&4=H-#0_Z>O_WI0Y#6.LX$Q3X'=8XASZKC"WY0 M"()`#&BI%X/U-:C5EUG`JY!CCM'!@!^+A\-!6,8Q5R%HDV,;;@ELT;2M+/93H+'[=D\F1F/HU55%[I,A$1^BQJ4:3$8T] M4^#]79L(7'1UF1B6HE^=V5U)Q7KKL^5F9?,@*K:\]L2])?17\"[W(!F`J2*# M,*`#C5F+UBZP'S0)$+P+?7/H._NK7/XJ+3BE!&^!];*9P(*!DG22A=YHR=`Y]Q]SB4JQO79)!N M&.E%^T69P$!R30]Y7*_@T#79.2.O#, MUOU'HY2Y^?>=^=V;2]M&A@^=5BPB]";7G@N??AIB%;3:I?)`7Q!U(46 M_4&#:A:I8;+?;E8IT1Q6_2(21-,N'ZLZ$BXXABW>X"YS-RH+++V\L`BW]&_@ M@E27YS[BV,M<=7&Y#)6#9`S-Y@YA+OU="Q[2!K1HRSE"^BM#%^K&0TV+J)6M MAW-!KB-[(#_7Y=E'$"9VJ#)K);"3(\OSX_)04.KPUTM[BH^BVS$#09E=Q>$7 M<>L=S5O.>TO8-=B+<22!O*Y.KB77!K:06P+[R'V!@^1+Y$L!4\`:L*&=1JK$ MVX10I,3'A9`+3E$,[SKJY;V13IHR$7$;8H`]V2^:$R0O4VE[(B'1=AH&V#O_ M9KU:8^.XJO"],[/S6GMW=G9G9Q\S^YCUSGJ]C]F'U^NUU^F:N+'K)":-"W92 M3`E1<0I-6R?@4*E"5GY@"R%4I"II48@PHOW#'U2E5BI5)6I=$TH%D0`31:EH M452>`@F!4(EWAW-WUU6+%`(2LYI[C^X]6_QX=7`L-.^@)H8_ M\=#;WPZY4PI56=5F>?GI#G/G'I$/Q(YP2]*BYY%]81^ M1CCC_W)D55CUKT6>0\]AE>=X0:C)L(%YU<]QLW(DHD6FL>0B4 M29X3!#\E7\8[&Y-JA$M0.I@O33Z=P)!J;RTL[P143^WMY6:@+?E;)%.#:HOH M%>>`PHJO=SM28&'`!D1<#9-CLPT*J:DX3#84U%(F&<&7!S."\]JE7C7I-[%6 MS*1;O^9%073QK9\F!X(%>CW*^@Q)UYJW\9OQ*6_*(]#1*%-;;!:\+M5#W3P2 MD]EHIU8=L/_D^`;@,X+YQE=-SBS4E%JX%A\Q6('C7;R;]PF%@)$VSOA6?4** M@N*2J5)5NLJPI4JH4*C)N4)8"VN5D$\!2GD>ZEABL;-R*5P!CUQN5C:,N)$K M5$IATFST3BHL/,#40H6V M$)*16`W73,W(47$S#B,O3<9,;(Y:6TL`,`'S;>GFPG)SJ6,O[RQTK&UR4M0_ M`GB=DS8W,](F1U#?A.(6"EQB`?Y+9,=^F`&`N[Q+@)FB.QT(68<7A1RP85P% MM_80?;D^TNO<>+%'RV=;P9C>NL*P;`_UF];[%.?HH5J_+,8L?"I?3`>2IRY1 M&9^OG,?K]%DNE%)RD582OZ@]J"9#K*X[S,F=/PH\RU!6\^<.#OIWG\QP0&(P MK2^-+[1NX;,]OI.97(+I\@BI#FC#>32*I<;+O^4P@QB,%.3': MF$\L^U>95<>&MJ&_P;Z7DO=Q4^XI:5)EABK51$7D6;'"JKPH5OR*DF;ATU@U MK?2GJPEHX1ZJ5L1J0JG)8KHF5\#M'/L\N\%NLXQJR0D6[FJB6JVD$ZHBLGQI M!+ME>D23/*,T8G6K1(M=UHRD,]SCHR468`>.L)=FSYID^?`Y`BI74:E^BZ?NT21 MZG.P&U%NC".8Y$;5;IP!?UR'^';"5/72A%%\PZQ4M,RH7APP\B'<^O_?^_+0_)-.:QEBI M?[2>F,E3FD91`=D['JN&/V/`MR MU>\V'CL:Q)RH!OH'TMEI82(\G?UD^$1V35S+/IM].?NKK&LJBU,9,9N!Z'!.HB:I MX1=*@;S8^X=7Z-X^+8J]Z;2[]<;A'/SN:"RWZAY]BF=85HUS"-^GS4&Q_C(4(%DA)%*7IBW.:L>!?1M?H&UL M0Q6I-]QHC$(A!Q5D'%^/7_IV().9N26]AZR#D,-@8)FV;^]@^_AQ\N00_+Z" MWL(R+N"C>(WR4_/T`,,RKS@..6ZP9SF)>Y4_P%\4ED6?^"VGZ;S:L]*[QS7@ MNN`VW-<]/L^._*R\[96]__0]I8C*-?\3_EOJU<"C@>W@,\%W0F^%E\-_UB[J MA_5?1+X3I:(78MFX%/^;\8SQ@W;6B,DK(!^\-5@X!#>+[GKA;D_1"#$.ED.( M[XX([59T]O2ZW))']L+*BE\-!$-A38]$8Y#B$+U`?4DSU9\>R&11+F\5BJ7R M8&6H.EP;&?U/_UJ_^XO]ORX&K4$;@;J-1BX4@[K"0B4T@NY#^]$1]"!:0(^@ M)]&YF->VP2^&^B$O(O,-F#_8GC^&OM"9M]^U;]C7[6W[9_:;]H_MJ_:/["W[ M=?LU^X5WTA\`>>>+OJL'CS[778=&,MHEAP%;[MHL6'V$84:`D0#LMXY-P;?- M=&T:/#[5M1FP5[HV"_;WQ@_-[+MW?^:!1TX^?#IW^/&3QQ[[;T;0.#H$Z^]# M]P(J&?0`8'82/8Q.H\/0+J(OH4F@,X:6X!O/ M(8*`!+\B0MSOV!_"&-YEY*\'0M]\R%W_._9T=O;KQ?V?W^WMK[4:W!<=UQ#9 M[EW_?PDP`(#,`-4-#65N9'-TW!4U1G_G7/OS280PB(0 M\B#DKI=$3'8%:2`)$%R2W00:'PD:NXL"N^1!>$0"9E(>`Y,1JG]^3L.=_Y MOO.=W_?[OG-W`P$@&6U0X*UM"C/]T:2_E9RA.6KZ@-#^])/@AD7Z"W9P82'R5^P]3 MUN\)-]4_LN/\5X!K%_$4-J^XM\6R+>%:;>N;5]4W^\Y_-I_^:.]8I+4091$R MM!J,5)J0`5C'V$^Q?Q6;9\6T`GABSUN?*$2`WPWT_L>%Y[$-KV,UUG-^'Z*8 M@#R4DY5G<0N"Z!%>3(+$8WB`=A>1A@HL$R=YQ@MHQ#NTRX$?.Y'*]3JTC$FSA*WV[,10WVRP[K"&[$+AP6+ZN*M96>;L!4-.%^M%LO MPH,2>FK#KX0A[K5Z,9^MB;@>QFY\8!UA7`X,B6.<0-1`&\F(79"!#W.FS!HT3V!HZ)!;)%Z;!\UFO6 MNW:NN#^7*(KQ<]R&56CA"3OQ9W3A.W&G3+'&6T]97=8!ZTO:2FC(0C;WE*"2 M?N=C,=KI-\J(/\0QMAY\+I+%=#%+5(E-8I%`B?>$IFR>ME@UPA]\LO547= MK/98I^-()#/A()-3B'PF;F:K(6^_1(2(MN(WS-T.(GL6W7B+F3F!7GR'2T(3 M#I$H)HB)]#Z'^#X4'\L4F2H-62I/*/G*3&6%^I[:H_EC[;'S5L`*6BNM5QC] MQSS+CMSFZ2XL(.(ZQM[*;&]@[NRVD>U!/(EG\!PK;`_^PI/_P;/?P1$G$!W^(2^H@B63C91HNQ;#G"0]9F,JM5HEJTB@VB36P4]XMV8GQ<[!.O MB(-DLD(&Y'RY7CXH7Y7OR??E1_*4/"N_49*4+,5%CM]4*]1YZHM:BK906Z>U M:7L2IO9=B!7&?A%;$&N-';(<5HJ59[5:ZZTGK"BS>B[.9"*&8PP,9B2?6;T9 MM[)5L=+F8Q%JT8!ES,UJLKF3?#[&")_#B\S3RZRE@XSN/6;].#YG9-_@>_0A M)B!4\IS.>LX3DQE1!2.Z0]2(@+A;+!`+18-H%"O%6K&.,6YF:Q-T"9J15J-5JP/F7O93\=*^5[D+K8:]9191R] M+[6.:FW,880W_AK>B$,XI2:)6_G^6*@4L'[K^&:9%+]]\$Z^<=+$&SSN_+SK M)UR7FS/>N-:E9X_+&IN9D9XV)G7TJ)'7C'`.3QF6/'1(4J(C05,5*>#V&^4A MWFE9<,/++W]EMY!2^'4 M9V"&QZW[#=T\Y#/TJ)A7'>#\(9\1U,W>^/R6^%S-C0O#*+A392%US>F<;`M_&:&X?.;Z88O MKE-R_.$ZLZHZX/=ENEQ!C]L49;7&(A-&J3D\?V![W+/I*#,3RNA:7V('@,UZ MI[L[LB7JQ*)0?G*=41>^.V`JX:!]Q(A\L[4G[CWAYYM\RH/R,2E/F ME(?K(^6D9O/L?C%D2^$ME"IOU^E3;@H&3+&)CG4;K@V]/XAZPV^OA);J9I)1 M:C1&EH;(>4;$Q-PUKKT9&=XNBU]N?CUR1\!PF3=E&L&P;VSG*$3FKOECNE=/ MOUKC<7>E;9CN(F5=GEF>6?8XW96VH7_\Y\;^]2/=0^-V^T]RK)P[R)JP@1AS M&(6IU^H$$#`82I']45^$2&T1S?@$!4E88B:5A2+.:3:G6H[3T"-?@VDT>L]> MO1(>6$G(<7X->VHG>[!@J+\\-_/SS;P\YISYJ6>:"&UF?&&*Q]UJ9AK-3MW, M)%6H(H_AX+2)Y-WELE.V.>K%(@IF6W6@7]:Q*',OO!/S@Z8,V9KNRYK1-;:F M[;)F<'O(8#7N@_T3;+29F#OX-]R9.M+?.,T4J3^BKH_KHYCLKHPBJ2K0*41[ M,"JL35'XLKJ0!&7A`JI_9I?[$A_CIU#@YD*>B[,I;KV3[:`>T2-SZB)Z MN=[(@E9SXB,5]9'@1(9^>V`)/^\(N$QO,'-P6A\,3J.?J;8?->XG$J2'I0,> MEL8]T$$?C0K=E4QR;E6@.F"V^3)-KR_(I/)^=)/6;M9!,$BKHD&D'-!>BHJTJ MKFHS7)GV@N$R7(05]/&HZ;P_EPLTBAD_SG#)E0S/)-J2.,,W_8\8]OX4AF?] M)(9+_SO#9<1<:C/L^_\Q[+^"8;O"$Q"S_Q'YI&]WW^[$C$3(G*N^'X>HGUJ] MDA.5_RS(XMB[')W:`8SA.%6%5:MDH4`6XQ9F*Y]W(O]5^5N1S!_'V7+[WJKB M[*C=] MSGN.'Y][[CEX>F!Z"I\GYT-XFDR'\'G^?`)/\],)+.+DI9"/F$0\E6HA1A%/ M`AA$?`Q`+^*C`+DBG@#0B7@<0"OB,0"-B(\`<"(^#*`6\2L`.2)^&2!;Q(<` M5")^"4`IXE$`5L0'`10B/@"0)>+]`'(1CP#(1+P/`":S%P")>!B`$?%01`N( M$&)42#JH*2.-1ER/]C#]#(=V4[^5^HW4&ZG742^_W,_]N)]KS$8?P/F?0W>H M[Z7>$-'TMW%]:N3^U, M^WB,^^T85S;&E8QQMC%HO7!9VZ9E5%?AS-,&"3Y,)5SD7?0^P\.O).B]%'^5 M-.:CFTQ(+M6O9W"6(12O,%%4"O@[II/B.4902NW;4PD_$=&V5*(>X-E48@O` MEE1B&T!W*K$#AO@^DZ!=.E/\(FG,11L8GJ9%YDF+G>9OABF@*R3.SY,F.QTX0F@@ MG*X%TVD#Z9J7T&Q54[2Q(OU+W/`379UT[DZ89FE$2U:3`5(4W46ZB(JHDE?1 M8;A>)=%HI)9-GF:3A]CD()O\(9OLW@2'[BL2Q MSY3&\=Y,:2\>HB5XB2])8P*F6AE&^JC,H-=F%$?AF#&#CA?,P"'F>+?%;!X* M6\+ZAMS:YMA_<=LSWOGTL7SG#LYO/Z@ML>\&+-,O0'J";E!_\0I+[K'D'98R MVC8"(4D)24I(2H3D/3:9(5AL,R=A;Y\Y:^N>J98*3VS=;3,>Z3PZB\.X/AZ; MQ0T2=&^>91[@<'R#U,X\B'4#;0NEP:X=!AH3D@!HZ"Q#)!I,YBRE]:9I/&Z0 M:`D)@(:'&9[2>#Q,:8L2[>)`*!Z[&`I1BOP:,T`I`_)KWZ),_2=EBE*F,I0" M2A$$H$0%B7*Q6`#"1:&8AE<_#7>FPYYTV$/#P:=A>SK;_HN M[/@/-C:9F7#8XM35H0I6/:.`6PM;\K]R#&8>*,(+@Z5[IJ(DJX:1P0)HBJCD M;)S)4L0Q?*/*(P:9C,E6L''$Y"NQ+)XE[U:MS*(?,3#4EW7+=>O!=RS7,>$Z MW3)4P555EN06Y0I@!D5`?!S*JOEJ3I3-?5TC??DQ0YY\)KLGFV(X)L[&^\#[YD&.H8CAV3#[A'H^]'56KO1J?VF_U6GU6?T',T533U,GOY,\4 MGN%GO:)/],]YYWQS?D-.43#(Z]5R%9:I@WI],$CT/&_-LU1B(YM)@ M5:4JVI`C5=9Y6JR*4&,SWVRWZIKX`1[S?$MV2W/%72IIK MARKJK7)P'=;<1,/*87'U>+=)9YZHJ40_3PY25 M%+,*D]'LK0X&_&5Y9H*"#2B,JLVL!K$R1286"".I-4^#2HK+_+Y`$((0HY5@ MP(L_;ZKX]:O[X]XW7SWD<>9Q66:Y(N=%E0S+Y?)G"TVEVAR529NK-&H:+'VC MM:6.`D[?U;`NZJO\WI%W;WTHL\:^6CB=6/>OCU.S#O-J33NG0ARKXK2:E5,_ MZ3IEUG!JM88U:"*FL>=\PNH)3^%@H+%`/S;RY\4E:?-<^6"E2]:;]0+C8XY' M`KLJ4;ZNV=7E&G+)W>5ZK<%`]`Y'.<;:JE6KS/XZ[6ZMHE0P:[.\ MOD`^?!]06\3D\-O=Y>6Z[8Y^QPF'S-'B\&<'_&F=ARIZ+,XZW6U)ZT?+NOO+ MH'$8E)>6D:1\A622SED@]&W=S8RZ&85\`I69];(ELNR,A-YJL\GXC?)!0TG0 M&PC21EFO2RAV&3C.M*.IU/-0\_#U-7=^WK)5$(HK3'GZKC7$^OM9S;7Z]A?/ MM#\OGZ]QVHQ57+;J5ST+T>7AE<;]XOVQ+]K/^=]=4, MO"FZEYA]Q'KA/MP[(3]+=?)F#+'E5.):^3-[?)8 M]G/NC;6[72.NP9JWY">SN9BM*,F\VVD$R(A$(V ME>\-OOJZ2O"P-F&M-C_8VJX.]3N33NQLUX9>BI^.XWA<$?*>ZP\F@SC8T5ZQ M<+]G<;FVHF=)=Q_LHR5)TN5'UOPEBR2FESP%PATW>>9TS4_ZC7P M&[>\%@KU'SLU[3!7.=[76D\.UFU>F1P\F,_7\FLCGIJ_7]@ZFC.Q4Z%X_%.M MU:"U%BS\;>'!J&)J*[$YO`7 M5EE<:[:].5?[;]:K/[:IXX[?>_=^V,_.\_GWLU_LYY_Q"[9Q8B>.XCB)'6=. M[,3&)"D55"GI:/C1P1)^166L%-8"!:V_8&PMJ!*L6Z?1_;%UW=32K:(B+&S+ M5&D%)D&G;@.DP11-FP32IA'OWK-#T;2VT[9[]MWW3E^?=9_[W.=SSURQ!;S? M/`,IE\ON&QD]^?B/GEX+U`N`O7J+/H7W9H1HS9SI6E%,%[M7K-@9W9D^&&7I M'C;7W!A:F43MP^VEY,KSQ=\4;Q1UY?**WE(I6YS.;90+_N+0<*Z-;@HB`Z-) M64I<1"X['4:&3O652UF&;C,B1\;A=1:<:,R`D&0*!IO:$@G)%(_3N;X^R93- MEB(=7*IC9&288_NR"3G.67)N77!4;D)[@P0*]@?'@D>";P3I8'"4H]%8_-'X M5^*OQW\4$(Q\)+HJ2T6U5U4C8VG$XKBIM&"VCA(+T\S.-S M@ENA%O`XJ"N4JF%.A0*UCRI8836V=PH`W5X(_X.X?1#Q3\QJTO=X@'>1K9\? M"Y8MA1=8QSKLK*)8ZO9WF'N(&E449?-_W%.>>I=M3W;8H3(/]$DMWO!4Y<6I M6-E\E.+-)M%J<71)W."1`8_-1],O0.@PY][H2[=F3[Q+0JO0^W97JMW3?OP< MI)*ER3]H=DZM>V8C/&3S#OMV'3B]^E1FP/;`W8\:1)/5XAX4^/6[D+/;X+.2 M+7JD$9R_V/C8\W\EY[1&K2#^^J'57UOS77).9]&%$/2A.+NX[EM?/%+SHF3U M%OPI]B(>-(*)S&">&M07&E9;5HDSU.Z&KS:\K/^EZ;SCBNF2XX;AINVFXX[A M[S:35J?5DZP>+T`\1%%(`07DS(6W:[8AS.7!7P(Q]53N*#B MNG4\6;.%NGQ9@0+N/=&_-EIY=<\73/[QEP_L(2N'WWGOZN'7SKS[VZ>WW/G@ M!T/+'[QQ^7WRS1]^Z>+\Q9,O7KWP*\6SURVN@6?A81`!W:":F4ZY\UV?2\^V M4FQCT)@P)EWM[@+8U?4S_A)_C;]AOA/1FRT6F\^?2`8"Q@@$_D@F/!%8Y@_S MT]25Q8 MN(ZIBW&YOG"?E=;)B15)I:=*UH\)"M""XK).M3VKTA47S2Q?YRR,W\_(4#!I M9PS$/0:K`L76W-=N]8)0C:GDDE&_DN[F%SFZ-<:9.)+H82`DD_V=&Z:V[IL[ M?W%9:ADO<,ZV$H;[VTAZH/"]N)SOC7S_P..+NZ-)^'[`H_5Z"-(7(S0\>VY- M;-7^0W^Z]`$R=VV(;#!?Y$!K`/\;&L+&,>XVJP,"_')K[DK1C%&J(YP_RE7NNU*#G&:)8A';8/O M/1A+)**21ZNG=)K0T90_+$:/O\8;W4%]P"&7WZ;A?"#][LT>.=@G( MQK!7GBP]63E*KFD;<;H]%/1J4$#!J52]13Y,/0Q"X#N9AV@7[::E5=)Z:4;: M+QV3-(S03]^T_LU*922OQU,0!!**)*0@9\[07@CM)#3;!;M=,D%!,I$DM!_C M+8R2FQ=S`1TIRQ"1>5+FFN6E:XFPI+`S'SJ[E?O>_%U"(2D*(YI-DQJ4!IB& MA!/-HPL:4J$H1OE"S-G]^S`H-KN;,!#*386I74UJ&MK4 M7B+A3U[2H,FI"02U-$=!@NA\57_Z31J9G3$QX^17/=656%ZTZLAW1)X-5[:9 M*9HD61US)7=WKB&5"E)J3`.&!1J@_5_G_'\6"E1PC?`#<>L!CX`- M8`N8!MO`CFJU/K(>CTS51JJ_KYZJOE)]J?J-ZM>KQ_XM/'B>ZE\^]3\U>$:B MGFL&2R!3.#;78P9'3DQB?UI9CR'.6%N/*1SOK\<,CE_/5LH# M_?GPV*8MD]NCA1V/;-ZT[C\;`ED,2!D,@'Z0!V$P!C;AQ4^"[6`$UQO`3K`9 M`[+M$[.BH`!VX(S->.23Y_IOLE1D.'`0K_(L1I!4]RP/`/M']O-X_<327EQZ M5KZVUI"^31@U:O]%LQ,C0@,"`V,C4@-C(U72]!7!E+T9O;G0^/@UE;F1O8FH-,30@,"!O M8FH\/"]3=6)T>7!E+U1R=654>7!E+T9O;G1$97-C7!E+T9O;G0^/@UE;F1O8FH-,34@,"!O8FH\/"].=6US M6S`@,38@,"!273X^#65N9&]B:@TQ-B`P(&]B:CP\+U,O1#X^#65N9&]B:@TQ M-R`P(&]B:CP\+T-O=6YT(#(O5'EP92]086=E7!E+UA-3"],96YG=&@@,S4U M,R]4>7!E+TUE=&%D871A/CYS=')E86T-"CP_>'!A8VME="!B96=I;CTB[[N_ M(B!I9#TB5S5-,$UP0V5H:4AZDY48WIK8SED(C\^"CQX.GAM<&UE=&$@ M>&UL;G,Z>#TB861O8F4Z;G,Z;65T82\B('@Z>&UP=&L](C,N,2TW,#$B/@H@ M("`\"UN&UL;G,Z9&,](FAT='`Z+R]P=7)L+F]R9R]D8R]E;&5M96YT"UD969A=6QT(CY- M:6-R;W-O9G0@5V]R9"`M($5-0D]34U]Q9RYD;V,\+W)D9CIL:3X*("`@("`@ M("`@("`@/"]R9&8Z06QT/@H@("`@("`@("`\+V1C.G1I=&QE/@H@("`@("`\ M+W)D9CI$97-C&UL;G,Z>&%P34T](FAT='`Z+R]N&%P+S$N,"]M;2\B/@H@("`@("`@("`\>&%P34TZ1&]C=6UE M;G1)1#YU=6ED.C9C,S9C93,W+3&%P34TZ1&]C=6UE;G1)1#X*("`@("`@("`@/'AA<$U-.DEN#IX;7!M971A/@H@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@"B`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`*("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@(`H@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@"B`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`*("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M(`H@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@"B`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`*("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@(`H@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M"B`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`*("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@(`H@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@"B`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`* M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@(`H@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@"B`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`*("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@(`H@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@"B`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@("`@ M("`@("`@("`@("`@("`@("`@("`*("`@("`@("`@("`@("`@("`@("`@("`@ M("`@"CP_>'!A8VME="!E;F0](G')E9@TP(#(P#3`P,#`P,#`P,#`@-C4U,S4@9@T*,#`P,#`V,S`U M.2`P,#`P,"!N#0HP,#`P,#8S,3DS(#`P,#`P(&X-"C`P,#`P-C,S,S@@,#`P M,#`@;@T*,#`P,#`W-C`W-R`P,#`P,"!N#0HP,#`P,#DQ-S4P(#`P,#`P(&X- M"C`P,#`P.3$Y-3@@,#`P,#`@;@T*,#`P,#$P.30R-2`P,#`P,"!N#0HP,#`P M,3`Y-C(X(#`P,#`P(&X-"C`P,#`Q,34X.#4@,#`P,#`@;@T*,#`P,#$Q-C`Y M,2`P,#`P,"!N#0HP,#`P,3$V,C0Y(#`P,#`P(&X-"C`P,#`Q,38U.3,@,#`P M,#`@;@T*,#`P,#$Q-S$P-B`P,#`P,"!N#0HP,#`P,3$W,C8T(#`P,#`P(&X- M"C`P,#`Q,3F4@,C`^/@US=&%R='AR968-,3$V '#24E14]�`` ` end debian/emboss-data.dirs0000644000000000000000000000002112214054043012234 0ustar usr/share/EMBOSS debian/emboss-doc.dirs0000644000000000000000000000002512214054043012074 0ustar usr/share/EMBOSS/doc debian/emboss-java.dirs0000644000000000000000000000004612214054043012253 0ustar usr/bin usr/share/EMBOSS/jemboss/org/ debian/emboss.mime0000644000000000000000000000141512214054043011323 0ustar application/vnd.appliedbiosystems.abif; abiview -auto '%s' ; description=ABIF Applied Biosystems Inc. chromatogram; nametemplate=%s.ab1 application/x-dna; abiview -auto '%s' ; description=ABIF Applied Biosystems Inc. chromatogram; nametemplate=%s.ab1 application/abi1; abiview -auto '%s' ; description=ABIF Applied Biosystems Inc. chromatogram; nametemplate=%s.ab1 application/vnd.appliedbiosystems.abif; seqret -filter '%s' ; description=ABIF Applied Biosystems Inc. chromatogram; nametemplate=%s.ab1 ; copiousoutput application/x-dna; seqret -filter '%s' ; description=ABIF Applied Biosystems Inc. chromatogram; nametemplate=%s.ab1 ; copiousoutput application/abi1; seqret -filter '%s' ; description=ABIF Applied Biosystems Inc. chromatogram; nametemplate=%s.ab1 ; copiousoutput debian/abiview.desktop0000644000000000000000000000106112214054043012200 0ustar [Desktop Entry] Version=1.0 Terminal=false #Icon=abiview Exec=abiview -outseq /dev/null -graph x11 %f Name=abiview GenericName=Chromatogram viewer GenericName[en]=Chromatogram viewer GenericName[fr]=Visualisateur de chromatogrammes Comment=Displays ABIF Applied Biosystems Inc. chromatograms. Comment[en]=Displays ABIF Applied Biosystems Inc. chromatograms. Comment[fr]=Affiche les chromatogrammes au format ABIF (Applied Biosystems Inc.). Type=Application Categories=Biology;Science;Education; MimeType=application/vnd.appliedbiosystems.abif; NoDisplay=true debian/changelog0000644000000000000000000005337712214054043011052 0ustar emboss (6.6.0-1) unstable; urgency=low [ Charles Plessy ] ec024a3 Imported Upstream version 6.5.7 78ef855 Removed upstream patch (for version 6.4.0). 2f66060 Clarified the license of the packaging. [ Andreas Tille ] * Imported Upstream version 6.6.0 (+adapt quilt patches) Closes: #558852 (at least the regexp dpkg-shlibdeps: warning: symbol.*found in none of the libraries does not appear in the build log any more - feel free to reopen with more info) * Clarified copyright and licenses for: - emboss/data/OBO/chebi.obo [b60238c] - emboss/data/OBO/gene_ontology*.obo [dc91819] - emboss/data/OBO/software.obo [3c8b4bf] - emboss/data/OBO/*.obo [8c34d40] - emboss/data/OBO/pathway.obo [1b3bbcf][1ff8ab9] - emboss/data/OBO/eco.obo [95aa795] - emboss/data/OBO/ro.obo [2865596] * debian/control: - Standards-Version: 3.9.4 (no changes needed) - Provide real package evince in addition to virtual package pdf-viewer * debian/rules: - Remove some remainings from CVS from emboss-test package * debian/{jemboss.desktop,jemboss.menu}: - runJemboss.sh is now POSIX shell instead of csh * debian/source/format: 3.0 (quilt) * debian/patches/bashism.patch: Avoid bashism Closes: #690651 -- Andreas Tille Mon, 09 Sep 2013 14:48:22 +0200 emboss (6.4.0-4) unstable; urgency=low * use autoreconf to enable latest changes -- Andreas Tille Fri, 10 Aug 2012 22:46:33 +0200 emboss (6.4.0-3) unstable; urgency=low * Import patches prepared by Felix Geyer to cope with the --as-needed issue when linking against database clients (thanks to Felix) Closes: #650237 * Fix typo to build emboss including PostgreSQL support (Thanks to Felix Geyer for the patch) Closes: #683190 -- Andreas Tille Thu, 09 Aug 2012 16:01:07 +0200 emboss (6.4.0-2) unstable; urgency=low * Separate architecture-dependant and independant targets in debian/rules. This makes the package buildable again on our build farm. -- Charles Plessy Thu, 21 Jun 2012 14:31:59 +0900 emboss (6.4.0-1) unstable; urgency=low [ Charles Plessy ] * New upstream release. * Removed calls to dh_makeshlibs in debian/rules (closes: #595613). * Build on libpng-dev instead of libpng12-dev (closes: #662313). * Breaks: EMBASSY <= 6.3.1 (debian/control). [ Andreas Tille ] * debian/upstream: separate reference section * debian/rules: - Make sure every binary package has a changelog file - enable hardening - do not clean backup file which is part of upstream tarball - remove executable flag from some test data - restore executable flag of some jemboss utils which seems to be removed by install target * debian/control: - remove article from description - Standards-Version: 3.9.3 (no changes needed) * debian/emboss.menu: delete - chances that users will pick command line programs from longish menu entries are pretty low * debian/emboss-lib.lintian-overrides: Adapted string of lintian warning -- Charles Plessy Wed, 20 Jun 2012 18:55:16 +0900 emboss (6.3.1-6) unstable; urgency=low * All EMBOSS libraries are to be considered private. The libajax* and libnucleus* are merged in the emboss-lib package, which is moved from the ‘libs’ to the ‘science’ section. Closes: #595613. * Added a Lintian override for the convenience copy of the PCRE library (debian/emboss-lib.lintian-overrides). * Build-depend on libhpdf-dev for PDF support, removed erroneous build dependance on libpcre3-dev (debian/control). * Added dependance on emboss to jemboss (debian/control). -- Charles Plessy Thu, 16 Sep 2010 21:06:14 +0900 emboss (6.3.1-5) unstable; urgency=low * New upstream patch, version 1-4. * Restore original config.* files in the clean target if the unpacked source package is a git repository (debian/rules). -- Charles Plessy Thu, 12 Aug 2010 08:00:58 +0900 emboss (6.3.1-4) unstable; urgency=low * New upstream patch, version 1-2. * Unset LS_COLORS in debian/rules (see #592089). -- Charles Plessy Sat, 07 Aug 2010 23:03:10 +0900 emboss (6.3.1-3) unstable; urgency=low * Use default Java instead of OpenJDK (debian/control, debian/rules, closes: #590553, thanks to Petr Salinger). * Incremented Standards-Version in debian/control to reflect conformance with Debian Policy 3.9.1 (no changes needed). -- Charles Plessy Wed, 28 Jul 2010 23:42:31 +0900 emboss (6.3.1-2) unstable; urgency=low * First upstream patch for version 6.3.1 (debian/series, debian/patches/official-upstream-patch.patch). * Moved openjdk-6-jdk to Build-Depends (debian/control, closes: #589897). -- Charles Plessy Fri, 23 Jul 2010 10:51:50 +0900 emboss (6.3.1-1) unstable; urgency=low * New upstream release. - Dropped debian/patches/official-upstream-patch.patch. - Refreshed the manual pages (debian/*manpages*). * Incremented Standards-Version in debian/control to reflect conformance with Debian Policy 3.9.0 (no changes needed). * Keep and restore a clean copy of the test directory, closes: #587170. * Build against Debian's zlib and expat libraries (debian/rules, debian/control, deleted debian/libajax6.lintian-overrides). * Added support for MySQL and PostgreSQL (debian/control, debian/rules). * Added symbols files for emboss-libs, libajax6 and libnucleus6. This will prevent mixing incompatible binary packages (LP: 526356). -- Charles Plessy Wed, 21 Jul 2010 15:24:07 +0900 emboss (6.2.0-2) unstable; urgency=low * Updated debian/patches/official-upstream-patch.patch to version 1-19. -- Charles Plessy Tue, 22 Jun 2010 17:01:44 +0900 emboss (6.2.0-1) unstable; urgency=low * New upstream release. * Dropped useless dependency on csh | c-shell for emboss (LP: 525662). * Incremented Standards-Version in debian/control to reflect conformance with Policy 3.8.4 (no changes needed). * Detected a zlib convenience copy; added debian/emboss.lintian-overrides until Upstream confirms that EMBOSS can build on latest pristine zlib (See http://lists.open-bio.org/pipermail/emboss/2010-May/003915.html). -- Charles Plessy Mon, 31 May 2010 15:13:09 +0900 emboss (6.1.0-5) unstable; urgency=low * The source package is now managed with Git (debian/control). - VCS URLs updated in debian/control. * debian/changelog: corrected an error on a program name (vectorstrip). * debian/patches/transient-vectorstrip.patch: keep quality scores. * Two new patches not yet officialised: - debian/patches/transient-vectorstrip.patch: retain quality scores. - debian/patches/tfm-html.patch: corrects path to HTML documentation. * Added Debian and FreeDesktop menu entries for Jemboss. * Do not create a makefile when there is not at clean time (debian/rules). * Documented how the package is tested in README.debian. * Added various informations about Upstream in debian/upstream-metadata.yaml -- Charles Plessy Mon, 09 Nov 2009 20:39:28 +0900 emboss (6.1.0-4) unstable; urgency=low * New upstream patch (patch-1-2): - Fix string extension so that pointers in lists remain valid. - This fixes a bug in processing SwissProt complex descriptions. - Fix definition of AJRESIZE0 macro. - Fix processing of first match in a profile alignment (prophet). * Delete /usr/share/EMBOSS/doc/programs/text/frestdist.txt, that should belong to embassy-phylip (PHYLIPNEW). (debian/rules) * Incremented Standards-Version in debian/control to reflect conformance with Policy 3.8.3 (no changes needed). * Removed the libtool libraries from the development packages (debian/rules). -- Charles Plessy Tue, 25 Aug 2009 23:19:10 +0900 emboss (6.1.0-2) unstable; urgency=low * New upstream patch (patch-1-1): - Fix feature specification problems in Jemboss. - Use version number to point to documentation URLs - Remove standalone option from server script. - Correct FASTQ input searching for '@' to start next sequence - Standardize FASTQ sequence formats with other OpenBio projects - Correct issues in igstrict, genpept and refseqp formats * debian/control: - Incremented Standards-Version to reflect conformance with Policy 3.8.2 (no changes needed). * debian/copyright.introduction: - Use symbolic links to refer to relevant versions of the GNU licenses. -- Charles Plessy Sat, 01 Aug 2009 10:26:26 +0900 emboss (6.1.0-1) unstable; urgency=low * New upstream release (Closes: #530112). * Dropped patch against previous release. * Created or refreshed the manpages. -- Charles Plessy Wed, 15 Jul 2009 23:15:26 +0900 emboss (6.0.1-11) unstable; urgency=low * New upstream patch (patch-1-12): - Remove the 'aligned' attribute that was added in Fix 4. - Fix crash if maxfragl > 40 selected. - Update Entrez retrieval to cope with an extra line added in the NCBI results. - For phylogenetic applications (PHYLIPNEW) reading distance matrix files failed for some formats written by other applications. Distance matrix input now works for multiple matrices in square, upper-triangular and lower-triangular formats. -- Charles Plessy Sun, 17 May 2009 14:51:05 +0900 emboss (6.0.1-10) unstable; urgency=low * New upstream patch (patch-1-8): Incorrect information was often given in the subsidiary table listing REs that would cut a greater number of times than an optional user-supplied maximum number. The main role of the program was unaffected. -- Charles Plessy Tue, 21 Apr 2009 13:01:38 +0900 emboss (6.0.1-9) unstable; urgency=low * New upstream patch (patch-1-7): - Corrections on syntax using the master qualifier name as a suffix. - Better support of the --without-x (not used in this package). - Bug corrected for needle and water using the -nobrief option. * debian/rules - Corrected again the targets to avoid calling them when it is not necessary. - Defines emboss_acdroot, emboss_docroot and emboss_data in order to run the tests. -- Charles Plessy Wed, 08 Apr 2009 20:20:58 +0900 emboss (6.0.1-8) unstable; urgency=low * debian/rules: - Do not pass java options to the configure script if openjdk is not installed (Closes: #521996, thanks to Peter Green). - Recursive removal of emboss_tmp (to build the package twice in a row). - Removed one `dh binary-indep` instance that strangely sneaked in after running `svn update`. * debian/control: - Moved again openjdk-6-jdk to Build-Depends-Indep. - Added debhelper's ${misc:Depends} substitution variable to the packages that did not already depend on it. -- Charles Plessy Tue, 31 Mar 2009 14:26:55 +0900 emboss (6.0.1-7) unstable; urgency=low * debian/control: moved openjdk-6-jdk to Build-Depends. Apologies to buildd administrators. (Closes: #521912). -- Charles Plessy Tue, 31 Mar 2009 08:34:59 +0900 emboss (6.0.1-6) unstable; urgency=low * debian/rules: - Build arch all packages only when binary-indep is called (Closes: #521398) - Corrected stamping gymnastics. * debian/control: moved openjdk-6-jdk to Build-Depends-Indep -- Charles Plessy Mon, 30 Mar 2009 13:02:11 +0900 emboss (6.0.1-5) unstable; urgency=low * New upstream patch (patch-1-6): correction for large pairwise alignments. * debian/control: - Incremented Standards-Version to reflect conformance with Policy 3.8.1 (no changes needed). - Moved the bibliographic reference from the description of the EMBOSS package to the file debian/reference. -- Charles Plessy Wed, 25 Mar 2009 11:44:30 +0900 emboss (6.0.1-4) unstable; urgency=low * New upstream patch (patch-1-5): - removes unnecessary whitespaces in edialign.acd. - saves Citations and comments in EMBL/GenBank formats for each new entry processed. * debian/control: - Uses the official homepage URL as confirmed by Upstream. - Redundant section field removed for jemboss. - Description corrected for libnucleus6-dev. * debian/rules: - Pass --bindir=/usr/lib/emboss directly instead of moving files. - Hardcode AJAX_FIXED_ROOT to /usr/share/EMBOSS (Closes: #487539). - Replaced `dh_clean -k', deprecated, by dh_prep. * debian/emboss.dir, debian/emboss.install: simplified after reworking the installation of the binaries and their symbolic links. -- Charles Plessy Sun, 22 Feb 2009 22:53:55 +0900 emboss (6.0.1-3) experimental; urgency=low * New upstream patch (patch-1-3). - fixes segmentation fault in vectorstrip when -auto is used with empty vectorsfile. - adds '.' trailer to the OS line in SwissProt output. * debian/rules: corrected the section of the manual pages of the renamed programs from 1 to 1e (Closes: #503733). * Preliminary support for jEMBOSS: - Build-Depend on openjdk-6-jdk (debian/control). - New package "jemboss", depending on openjdk-6-jre (debian/control). - The jemboss package contains everything installed by the command `make -C jemboss install' (debian/rules). -- Charles Plessy Wed, 26 Nov 2008 08:57:20 +0900 emboss (6.0.1-2) experimental; urgency=low * New upstream patch (patch-1-1). - jaspscan can now scan multiple sequences. - "digest -allpartials" now reports all C-term fragments. -- Charles Plessy Wed, 27 Aug 2008 22:11:45 +0900 emboss (6.0.1-1) experimental; urgency=low * New upstream release: - New applications: aligncopy, aligncopypair, consambig, density, featcopy, featreport, infobase, inforesidue, jaspextract, jaspscan, maskambignuc, maskambigprot, nohtml, nospace, notab, sizeseq, skipredundant, trimspace. - See `/usr/share/doc/emboss/changelog.gz' for more details. * debian/patches: - Removed the patches that are obsoleted by the new release. - Documented the local patch on `tfm' that changes default pager. * debian/README.source added to document how to patch and unpatch the sources. * debian/emboss-doc.doc-base.{apps/groups} corrected for new file locations. * debian/control: - Replaced build dependency on deprecated x-dev by x11proto-core-dev. - Uses debhelper 7. - Incremented the soname of the AJAX and NUCLEUS libraries (conflict and replace the previous versions). - Incremented Standards-Version to 3.8.0 after adding README.Sources. - Added a new package, emboss-test, that contains test data. - Build-Depends: tcsh | csh | c-shell to run the tests. * debian/rules: - Implemented build-time tests. - Updated the instructions to build manpages. -- Charles Plessy Thu, 17 Jul 2008 14:07:40 +0900 emboss (5.0.0-7) unstable; urgency=low * Changed the doc-base section according to the new policy. * Updated my email address. * Updated the contact address in the manpages. -- Charles Plessy Fri, 16 May 2008 19:58:37 +0900 emboss (5.0.0-6) unstable; urgency=low * New bugfixes released upstream: - Fixes failure on some databases if the PAGESIZE was set large and the CACHESIZE was set small. - Platform-independence modifications added. * debian/README.Debian: described the change of default pager for tfm. -- Charles Plessy Fri, 07 Mar 2008 10:15:31 +0900 emboss (5.0.0-5) unstable; urgency=low * New bugfixes released upstream. - Fixes changed ID format in GCG databases. - Fixes reading from PIR databases. - Fixes a problem with O in protein sequences for pyrrolysine. - Fixes a problem in GENBANK output format. - Fixes a problem in reading protein sequences from Staden "spin" interface. - Fixes tokens that are longer than the maximum length. - debian/patches now uses the monolithic upstream patch instead of file-per-file fixes. You can find longer explanations in the header of debian/patches/patch-1-3. -- Charles Plessy Sat, 01 Mar 2008 11:46:26 +0900 emboss (5.0.0-4) unstable; urgency=low * debian/patches: - using-pager-in-tfm.patch: Patching tfm so that it uses the alternatives system `/usr/bin/pager' if the `PAGER' environment variable is not defined. - embindex-fix-2008-01-19.patch: Official fix 3. EMBOSS-5.0.0/nucleus/embindex.c 18 Jan 2008. Order and fill fixes to sort out potential problems with kw/de/tx indexes. -- Charles Plessy Wed, 23 Jan 2008 20:56:22 +0900 emboss (5.0.0-3) unstable; urgency=low [ Nelson A. de Oliveira ] * Using bzip2 compression for packages. This saves about 832KB of space. [ Charles Plessy ] * debian/patches/ajindex-fix-2008-01-09.patch: - Fixes rare secondary index problem with input files over 2Gb. * debian/control: - Switched maintainership to the Debian-Med packaging team. - Relocated the package to the Debian-Med Subversion repository. - Allowed upload by Debian Maintainers. - Checked that the package is compliant to Policy 3.7.3 - Added dialign again to the Recommends: field. It only disappeared from the documentation; the edialign program is still there. - -dev packages now depend on their corresponding libraries. - Replaced occurrences of $(source:Version} by ${binary:Version} to make the packages binNMU safe. - emboss-data and emboss-doc do not Suggest: emboss anymore. - Changed the description of libajax5 and libnucleus5 so that they are not identical. - Removed the XS- prefix in the Vcs fields. - Build-depends on autotools-dev. * debian/rules: - Removes Makefiles ignored by make distclean in the test directory. - Uses config.(sub|guess) from the autotools-dev package. -- Charles Plessy Thu, 10 Jan 2008 21:27:31 +0900 emboss (5.0.0-2) unstable; urgency=low [ Charles Plessy ] * Using a emboss/psiphi.c file fixed by upstream ftp://emboss.open-bio.org/pub/EMBOSS/fixes/psiphi.c * Documentation: - Building the manpages offline to save buildd time, therefore not depending anymore on the XML toolchain. - Added a "e" suffix to the manpages, to avoid conflicts. (Closes: #427439) - Linked /usr/share/emboss-doc/doc/ to /usr/share/EMBOSS/docs, and registered documentation in doc-base. (Closes: #423941) * Gave their own packages to the AJAX and NUCLEUS libraries. - Header files are in /usr/include/ajax and /usr/include/nucleus. - The private pcre files are kept under /usr/include/ajax. (Closes: #433316) * Packaging: - Removed the extra Tag field in debian/control. - Removed the recommendation on dialign, as edialign disappeared. - Tightened the Depends: relationship between emboss and emboss-lib (Closes: #435232). - Removed inactive developer from the uploaders list. - Suggests: embassy. * Temporarily incorporates a relicenced version of the EMBOSS Quick Guide, until it becomes part of the original tarball. Its sources are shipped uuencoded, therefore emboss now build-depends on sharutils. [ Nelson A. de Oliveira ] * Checked and fixed clean target. (Closes: #442554). -- Charles Plessy Sat, 13 Oct 2007 15:05:53 +0900 emboss (5.0.0-1) unstable; urgency=low * New upstream version * Renaming cons and pscan to em_cons and em_pscan, see README.Debian for more information. * Moved all the binaries to /usr/lib/emboss. /usr/bin contains only symbolic links (Closes : #427439, #427440). * Makes sure that there is a Makefile before invoking the clean rule. * Added /etc/emboss/embossrc.d directory for future modular configuration. * Switched from dpatch to quilt (no patches for the moment). * Build-depend on libemboss-acd-perl to generate manpages with acd2docbook.pl, written especially for this package (Closes: #423938). * Adding a placeholder file to force the inclusion of debian/manpages. * Removing the entries in the Debian menu until we agree that we want them. -- Charles Plessy Thu, 19 Jul 2007 13:56:11 +0900 emboss (4.1.0-1) experimental; urgency=low * New maintainer and uploaders * First official release (Closes: #156276) * Xlib transition. * Using dpatch and /usr/share/dpatch/dpatch.make to manage patches. * Added XS-Vcs entries in debian/changelog. * Removed the pcre includes from the emboss-libs package. * Fixed watch file. * Emboss Recommends:dialign and Suggests:clustalw. -- Charles Plessy Mon, 12 Mar 2007 08:26:15 +0900 emboss (2.8.0-2) unstable; urgency=low * Fixed manpages being in both emboss and emboss-lib * Removed circ.dep. emboss <-> emboss-lib -- Matt Hope Fri, 21 May 2004 12:47:47 +1000 emboss (2.8.0-1) unstable; urgency=low * New upstream release -- Matt Hope Fri, 5 Dec 2003 15:08:54 +1100 emboss (2.7.1-1) unstable; urgency=low * New upstream release * emboss-lib - Fixed the shlibs. -- Matt Hope Mon, 7 Jul 2003 14:36:14 +1000 emboss (2.6.0-1) unstable; urgency=low * New upstream release -- Matt Hope Fri, 7 Apr 2003 21:41:12 +1000 emboss (2.4.1-1) unstable; urgency=low * Initial package. Thanks for the feedback from everyone. (Closes: Bug#156276 ITP) -- Matt Hope Sat, 6 Jul 2002 01:11:17 +1000 debian/patches/0000755000000000000000000000000012214054043010610 5ustar debian/patches/tfm-html.patch0000644000000000000000000000104112214054043013355 0ustar Author: Charles Plessy Forwarded: https://sourceforge.net/tracker/?func=detail&aid=2877960&group_id=93650&atid=605031 Description: Corrects the name of the directory where tfm looks for HTML documentation. --- a/emboss/tfm.c +++ b/emboss/tfm.c @@ -231,7 +231,7 @@ static void tfm_FindAppDocRoot(const AjP ** if that didn't work then try the doc directory from the ** distribution tarball */ - ajStrAssignS(docroot, ajNamValueBasedir()); + ajStrAssignS(docroot, ajNamValueRootdir()); ajDirnameFix(docroot); if(ajStrGetLen(embassy)) debian/patches/using-pager-in-tfm.patch0000644000000000000000000000124712214054043015246 0ustar Author: Charles Plessy Forwarded: no This patch uses a specificity of Debian. Description: Browse the documentation with default pager. `/usr/bin/pager', always exists in Debian and is managed through the alternatives system. With this patch, `tfm' will use `/usr/bin/pager' by default, which points on the user's favorite pager. License: as if it were public domain. --- a/emboss/tfm.c +++ b/emboss/tfm.c @@ -87,7 +87,7 @@ int main(int argc, char **argv) if(shellpager) ajStrAssignC(&pager,shellpager); if(!ajStrGetLen(pager)) - ajStrAssignC(&pager,"more"); + ajStrAssignC(&pager,"pager"); } ajFmtPrintS(&cmd,"%S %S",pager,path); ajSysExecPathS(cmd); debian/patches/bashism.patch0000644000000000000000000000106512214054043013261 0ustar Author: Andreas Tille Date: Mon, 09 Sep 2013 14:48:22 +0200 BugsDebian: http://bugs.debian.org/690651 Description: Avoid bashism --- a/jemboss/utils/install-jemboss-server.sh +++ b/jemboss/utils/install-jemboss-server.sh @@ -287,7 +287,7 @@ ssl_print_notes() TCVERSION=`sed -n -e 's|\(.*\)Running The Apache Tomcat 6.0\(.*\)|6|p' $TOMCAT_ROOT/RUNNING.txt` - if [ "$TCVERSION" == "6" ]; then + if [ "$TCVERSION" = "6" ]; then #tomcat 6.x echo echo ' ' debian/patches/series0000644000000000000000000000014712214054043012027 0ustar using-pager-in-tfm.patch tfm-html.patch fix-postgresql-macro.patch fix-mysql-macro.patch bashism.patch debian/patches/fix-mysql-macro.patch0000644000000000000000000000170112214054043014660 0ustar Description: Enable linking mysqlclient with linker set for --as-needed Author: Felix Geyer Date: Sun, 29 Jul 2012 22:07:33 +0200 Bugs-Debian: http://bugs.debian.org/650237 LastChanged: Mon, 09 Sep 2013 14:48:22 +0200 (Andreas Tille, adapt to 6.6.0) --- a/m4/mysql.m4 +++ b/m4/mysql.m4 @@ -101,10 +101,10 @@ AC_DEFUN([AX_LIB_MYSQL], dnl not be installed EMBCPPFLAGS="${CPPFLAGS}" - EMBLDFLAGS="${LDFLAGS}" + EMBLIBS="${LIBS}" CPPFLAGS="${MYSQL_CPPFLAGS} ${EMBCPPFLAGS}" - LDFLAGS="${MYSQL_LDFLAGS} ${EMBLDFLAGS}" + LIBS="${MYSQL_LDFLAGS} ${EMBLIBS}" AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include #include "mysql.h"]], @@ -113,7 +113,7 @@ AC_DEFUN([AX_LIB_MYSQL], [havemysql="no"]) CPPFLAGS="${EMBCPPFLAGS}" - LDFLAGS="${EMBLDFLAGS}" + LIBS="${EMBLIBS}" AS_IF([test "x${havemysql}" = "xyes"], [ debian/patches/fix-postgresql-macro.patch0000644000000000000000000000175712214054043015731 0ustar Description: Enable linking pgsqlclient with linker set for --as-needed Author: Felix Geyer Date: Sun, 29 Jul 2012 22:07:33 +0200 Bugs-Debian: http://bugs.debian.org/650237 LastChanged: Mon, 09 Sep 2013 14:48:22 +0200 (Andreas Tille, adapt to 6.6.0) --- a/m4/postgresql.m4 +++ b/m4/postgresql.m4 @@ -98,10 +98,10 @@ AC_DEFUN([AX_LIB_POSTGRESQL], dnl not be installed EMBCPPFLAGS="${CPPFLAGS}" - EMBLDFLAGS="${LDFLAGS}" + EMBLIBS="${LIBS}" CPPFLAGS="${POSTGRESQL_CPPFLAGS} ${EMBCPPFLAGS}" - LDFLAGS="${POSTGRESQL_LDFLAGS} ${EMBLDFLAGS}" + LIBS="${POSTGRESQL_LDFLAGS} ${EMBLIBS}" AC_LINK_IFELSE([AC_LANG_PROGRAM([[#include #include "libpq-fe.h"]], @@ -110,7 +110,7 @@ AC_DEFUN([AX_LIB_POSTGRESQL], [havepostgresql="no"]) CPPFLAGS="${EMBCPPFLAGS}" - LDFLAGS="${EMBLDFLAGS}" + LIBS="${EMBLIBS}" AS_IF([test "x${havepostgresql}" = "xyes"], [ debian/emboss.install0000644000000000000000000000011512214054043012036 0ustar debian/emboss_tmp/usr/lib usr #debian/abiview.desktop usr/share/applications debian/build-manpages.sh0000755000000000000000000000113012214054043012403 0ustar #!/bin/sh -e # Copyleft 2007 Charles Plessy, do what you want with this trivial file. PACKAGE=$(dpkg-parsechangelog -ldebian/changelog | grep Source: | cut -f2 -d' ') VERSION=$(dpkg-parsechangelog -ldebian/changelog | grep Version: | cut -f2 -d' ' | cut -f1 -d-) ORIGTARGZ=../${PACKAGE}_${VERSION}.orig.tar.gz rm -f debian/$PACKAGE.manpages for FILE in $(ls emboss/acd/*.acd) do ACD=$(basename $FILE .acd) ./debian/acd2docbook.pl $FILE ${VERSION} \ | xsltproc --nonet --param man.charmap.use.subset 0 -o debian/manpages/ - echo "debian/manpages/$ACD.1e" >> debian/$PACKAGE.manpages done debian/compat0000644000000000000000000000000212214054043010357 0ustar 9 debian/emboss-test.dirs0000644000000000000000000000004712214054043012312 0ustar usr/share/EMBOSS etc/emboss/embossrc.d debian/emboss-data.install0000644000000000000000000000005512214054043012750 0ustar debian/emboss_tmp/usr/share/EMBOSS usr/share debian/emboss.manpages0000644000000000000000000002140412214054043012167 0ustar debian/manpages/aaindexextract.1e debian/manpages/abiview.1e debian/manpages/acdc.1e debian/manpages/acdlog.1e debian/manpages/acdpretty.1e debian/manpages/acdrelations.1e debian/manpages/acdtable.1e debian/manpages/acdtrace.1e debian/manpages/acdvalid.1e debian/manpages/ajbad.1e debian/manpages/ajfeatest.1e debian/manpages/ajtest.1e debian/manpages/aligncopy.1e debian/manpages/aligncopypair.1e debian/manpages/antigenic.1e debian/manpages/backtranambig.1e debian/manpages/backtranseq.1e debian/manpages/banana.1e debian/manpages/biosed.1e debian/manpages/btwisted.1e debian/manpages/cachedas.1e debian/manpages/cachedbfetch.1e debian/manpages/cacheebeyesearch.1e debian/manpages/cacheensembl.1e debian/manpages/cai.1e debian/manpages/chaos.1e debian/manpages/charge.1e debian/manpages/checktrans.1e debian/manpages/chips.1e debian/manpages/cirdna.1e debian/manpages/codcmp.1e debian/manpages/codcopy.1e debian/manpages/coderet.1e debian/manpages/complex.1e debian/manpages/compseq.1e debian/manpages/cons.1e debian/manpages/consambig.1e debian/manpages/corbatest.1e debian/manpages/cpgplot.1e debian/manpages/cpgreport.1e debian/manpages/cusp.1e debian/manpages/cutgextract.1e debian/manpages/cutseq.1e debian/manpages/dan.1e debian/manpages/dastest.1e debian/manpages/dbfetchtest.1e debian/manpages/dbget.1e debian/manpages/dbgeturl.1e debian/manpages/dbiblast.1e debian/manpages/dbifasta.1e debian/manpages/dbiflat.1e debian/manpages/dbigcg.1e debian/manpages/dbshowdat.1e debian/manpages/dbshowquery.1e debian/manpages/dbtell.1e debian/manpages/dbtellquery.1e debian/manpages/dbxcompress.1e debian/manpages/dbxedam.1e debian/manpages/dbxfasta.1e debian/manpages/dbxflat.1e debian/manpages/dbxgcg.1e debian/manpages/dbxobo.1e debian/manpages/dbxreport.1e debian/manpages/dbxresource.1e debian/manpages/dbxstat.1e debian/manpages/dbxtax.1e debian/manpages/dbxuncompress.1e debian/manpages/degapseq.1e debian/manpages/density.1e debian/manpages/descseq.1e debian/manpages/diffseq.1e debian/manpages/digest.1e debian/manpages/distmat.1e debian/manpages/docxmlvalid.1e debian/manpages/docxmlwell.1e debian/manpages/domtesta.1e debian/manpages/domtestb.1e debian/manpages/domtestc.1e debian/manpages/domtestd.1e debian/manpages/dotmatcher.1e debian/manpages/dotpath.1e debian/manpages/dottup.1e debian/manpages/dreg.1e debian/manpages/drfinddata.1e debian/manpages/drfindformat.1e debian/manpages/drfindid.1e debian/manpages/drfindresource.1e debian/manpages/drget.1e debian/manpages/drtext.1e debian/manpages/edamclean.1e debian/manpages/edamdef.1e debian/manpages/edamhasinput.1e debian/manpages/edamhasoutput.1e debian/manpages/edamisformat.1e debian/manpages/edamisid.1e debian/manpages/edamname.1e debian/manpages/edialign.1e debian/manpages/einverted.1e debian/manpages/embossdata.1e debian/manpages/embossversion.1e debian/manpages/emma.1e debian/manpages/emowse.1e debian/manpages/ensembltest.1e debian/manpages/entrails.1e debian/manpages/entrailsbook.1e debian/manpages/entrailshtml.1e debian/manpages/entrailswiki.1e debian/manpages/entret.1e debian/manpages/entrygo.1e debian/manpages/entrytax.1e debian/manpages/epestfind.1e debian/manpages/eprimer32.1e debian/manpages/eprimer3.1e debian/manpages/equicktandem.1e debian/manpages/est2genome.1e debian/manpages/etandem.1e debian/manpages/extractalign.1e debian/manpages/extractfeat.1e debian/manpages/extractseq.1e debian/manpages/featcopy.1e debian/manpages/featreport.1e debian/manpages/feattext.1e debian/manpages/findkm.1e debian/manpages/freak.1e debian/manpages/fuzznuc.1e debian/manpages/fuzzpro.1e debian/manpages/fuzztran.1e debian/manpages/garnier.1e debian/manpages/geecee.1e debian/manpages/getorf.1e debian/manpages/godef.1e debian/manpages/goname.1e debian/manpages/goseq.1e debian/manpages/helixturnhelix.1e debian/manpages/histogramtest.1e debian/manpages/hmoment.1e debian/manpages/idtell.1e debian/manpages/iep.1e debian/manpages/infoalign.1e debian/manpages/infobase.1e debian/manpages/inforesidue.1e debian/manpages/infoseq.1e debian/manpages/intconv.1e debian/manpages/isdbdata.1e debian/manpages/isdbname.1e debian/manpages/isochore.1e debian/manpages/jaspextract.1e debian/manpages/jaspscan.1e debian/manpages/lindna.1e debian/manpages/listor.1e debian/manpages/makenucseq.1e debian/manpages/makeprotseq.1e debian/manpages/marscan.1e debian/manpages/martattributes.1e debian/manpages/martdatasets.1e debian/manpages/martfilters.1e debian/manpages/martquery.1e debian/manpages/martregistry.1e debian/manpages/martseqs.1e debian/manpages/maskambignuc.1e debian/manpages/maskambigprot.1e debian/manpages/maskfeat.1e debian/manpages/maskseq.1e debian/manpages/matcher.1e debian/manpages/megamerger.1e debian/manpages/merger.1e debian/manpages/msbar.1e debian/manpages/mwcontam.1e debian/manpages/mwfilter.1e debian/manpages/needle.1e debian/manpages/needleall.1e debian/manpages/newcoils.1e debian/manpages/newcpgreport.1e debian/manpages/newcpgseek.1e debian/manpages/newseq.1e debian/manpages/nohtml.1e debian/manpages/noreturn.1e debian/manpages/nospace.1e debian/manpages/notab.1e debian/manpages/notseq.1e debian/manpages/nthseq.1e debian/manpages/nthseqset.1e debian/manpages/octanol.1e debian/manpages/oddcomp.1e debian/manpages/ontocount.1e debian/manpages/ontoget.1e debian/manpages/ontogetcommon.1e debian/manpages/ontogetdown.1e debian/manpages/ontogetobsolete.1e debian/manpages/ontogetroot.1e debian/manpages/ontogetsibs.1e debian/manpages/ontogetup.1e debian/manpages/ontoisobsolete.1e debian/manpages/ontotext.1e debian/manpages/origsplitter.1e debian/manpages/origunion.1e debian/manpages/palindrome.1e debian/manpages/pasteseq.1e debian/manpages/patmatdb.1e debian/manpages/patmatmotifs.1e debian/manpages/patmattest.1e debian/manpages/pepcoil.1e debian/manpages/pepdigest.1e debian/manpages/pepinfo.1e debian/manpages/pepnet.1e debian/manpages/pepstats.1e debian/manpages/pepwheel.1e debian/manpages/pepwindow.1e debian/manpages/pepwindowall.1e debian/manpages/plotcon.1e debian/manpages/plotorf.1e debian/manpages/polydot.1e debian/manpages/preg.1e debian/manpages/prettyplot.1e debian/manpages/prettyseq.1e debian/manpages/prima.1e debian/manpages/primers.1e debian/manpages/primersearch.1e debian/manpages/printsextract.1e debian/manpages/profit.1e debian/manpages/prophecy.1e debian/manpages/prophet.1e debian/manpages/prosextract.1e debian/manpages/pscan.1e debian/manpages/psiphi.1e debian/manpages/rebaseextract.1e debian/manpages/recoder.1e debian/manpages/redata.1e debian/manpages/remap.1e debian/manpages/restover.1e debian/manpages/restrict.1e debian/manpages/revseq.1e debian/manpages/seealso.1e debian/manpages/seqcount.1e debian/manpages/seqgo.1e debian/manpages/seqinfo.1e debian/manpages/seqmatchall.1e debian/manpages/seqret.1e debian/manpages/seqretall.1e debian/manpages/seqretallfeat.1e debian/manpages/seqretset.1e debian/manpages/seqretsetall.1e debian/manpages/seqretsingle.1e debian/manpages/seqretsplit.1e debian/manpages/seqrettype.1e debian/manpages/seqtax.1e debian/manpages/seqxref.1e debian/manpages/seqxrefall.1e debian/manpages/seqxrefget.1e debian/manpages/servertell.1e debian/manpages/showalign.1e debian/manpages/showdb.1e debian/manpages/showfeat.1e debian/manpages/showorf.1e debian/manpages/showpep.1e debian/manpages/showseq.1e debian/manpages/showserver.1e debian/manpages/shuffleseq.1e debian/manpages/sigcleave.1e debian/manpages/silent.1e debian/manpages/sirna.1e debian/manpages/sixpack.1e debian/manpages/sizeseq.1e debian/manpages/skipredundant.1e debian/manpages/skipseq.1e debian/manpages/splitsource.1e debian/manpages/splitter.1e debian/manpages/sqltest.1e debian/manpages/stretcher.1e debian/manpages/stssearch.1e debian/manpages/supermatcher.1e debian/manpages/syco.1e debian/manpages/taxget.1e debian/manpages/taxgetdown.1e debian/manpages/taxgetrank.1e debian/manpages/taxgetspecies.1e debian/manpages/taxgetup.1e debian/manpages/taxseq.1e debian/manpages/tcode.1e debian/manpages/testplot.1e debian/manpages/textget.1e debian/manpages/textsearch.1e debian/manpages/texttotext.1e debian/manpages/texttoxml.1e debian/manpages/textvalid.1e debian/manpages/tfextract.1e debian/manpages/tfm.1e debian/manpages/tfscan.1e debian/manpages/tmap.1e debian/manpages/tranalign.1e debian/manpages/transeq.1e debian/manpages/treetypedisplay.1e debian/manpages/trimest.1e debian/manpages/trimseq.1e debian/manpages/trimspace.1e debian/manpages/twofeat.1e debian/manpages/union.1e debian/manpages/urlget.1e debian/manpages/vectorstrip.1e debian/manpages/water.1e debian/manpages/whichdb.1e debian/manpages/wobble.1e debian/manpages/wordcount.1e debian/manpages/wordfinder.1e debian/manpages/wordmatch.1e debian/manpages/wossdata.1e debian/manpages/wossinput.1e debian/manpages/wossname.1e debian/manpages/wossoperation.1e debian/manpages/wossoutput.1e debian/manpages/wossparam.1e debian/manpages/wosstopic.1e debian/manpages/xmltotext.1e debian/manpages/xmltoxml.1e debian/manpages/xmltransform.1e debian/manpages/yank.1e debian/jemboss.desktop0000644000000000000000000000040312214054043012213 0ustar [Desktop Entry] Version=1.0 Terminal=false Icon=jemboss Exec=runJemboss.sh Name=Jemboss GenericName=GUI for EMBOSS Comment=Graphical user interface for the European Molecular Biology Open Software Suite. Type=Application Categories=Biology;Science;Education; debian/jemboss.install0000644000000000000000000000005612214054043012214 0ustar debian/jemboss.desktop usr/share/applications