debian/0000755000000000000000000000000012241433525007167 5ustar debian/control0000644000000000000000000000361312241426147010577 0ustar Source: glam2 Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Charles Plessy , Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9), libfftw3-dev Standards-Version: 3.9.4 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/glam2/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/glam2/trunk/ Homepage: http://bioinformatics.org.au/glam2/ Package: glam2 Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Description: gapped protein motifs from unaligned sequences GLAM2 is a software package for finding motifs in sequences, typically amino-acid or nucleotide sequences. A motif is a re-occurring sequence pattern: typical examples are the TATA box and the CAAX prenylation motif. The main innovation of GLAM2 is that it allows insertions and deletions in motifs. . This package includes programs for discovering motifs shared by a set of sequences and finding matches to these motifs in a sequence database, as well as utilities for converting glam2 motifs to standard alignment formats, masking glam2 motifs out of sequences so that weaker motifs can be found, and removing highly similar members of a set of sequences. . The package includes these programs: glam2: discovering motifs shared by a set of sequences; glam2scan: finding matches, in a sequence database, to a motif discovered by glam2; glam2format: converting glam2 motifs to standard alignment formats; glam2mask: masking glam2 motifs out of sequences, so that weaker motifs can be found; glam2-purge: removing highly similar members of a set of sequences. . In this binary package, the fast Fourier algorithm (FFT) was enabled for the glam2 program. debian/NEWS.Debian0000644000000000000000000000222012241432564011045 0ustar glam2 (1064-3) unstable; urgency=low The source of glam2 is now maintained in the MEME software suite at http://meme.nbcr.net/meme/ Since MEME is non-free we are keeping this old source here and once the packaging of MEME is finished (packaging started at svn://anonscm.debian.org/debian-med/trunk/packages/meme/trunk/ by Debian Med team) an alternative might be provided. There is an alternative branch svn://anonscm.debian.org/debian-med/trunk/packages/glam2/branch/meme in SVN which strips the glam2 source from MEME which might or might not be considered free. At least MEME authors agreed on the idea that glam2 license should be valid also at the new place on the Debian Med packaging mailing list in February 2013. However, it has turned out that some additional tools of the MEME suite are needed to successfully build glam2 and this was not yet discussed. If you are interested feel free to test the glam2 packaging in branch/meme and in case the test turns out to be successful please ask the authors for permission for relicensing. -- Andreas Tille Fri, 15 Nov 2013 15:07:59 +0100 debian/install0000644000000000000000000000016611736403523010566 0ustar src/glam2format /usr/bin/ src/glam2mask /usr/bin/ src/glam2scan /usr/bin/ src/glam2fft /usr/bin/ purge/purge /usr/bin debian/glam2.1.xml0000644000000000000000000002047511736403523011065 0ustar ]> &dhtitle; &dhproduct; &dhrelease; Martin C Frith Author of GLAM2. Timothy L Bailey Author of GLAM2. &dhfirstname; &dhsurname; Formatted this manpage in DocBook XML for the Debian distribution.
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The source code and the documentation of GLAM2 are released in the public domain. &dhucpackage; &dhsection; &dhpackage; Gapped Local Alignment of Motifs &dhpackage; my_seqs.fa An alphabet other than p or n is interpreted as the name of an alphabet file. DESCRIPTION GLAM2 is a software package for finding motifs in sequences, typically amino-acid or nucleotide sequences. A motif is a re-occurring sequence pattern: typical examples are the TATA box and the CAAX prenylation motif. The main innovation of GLAM2 is that it allows insertions and deletions in motifs. OPTIONS (default settings) Show all options and their default settings. Output file (stdout). Number of alignment runs (10). End each run after this many iterations without improvement (10000). Examine both strands - forward and reverse complement. Minimum number of sequences in the alignment (2). Minimum number of aligned columns (2). Maximum number of aligned columns (50). Initial number of aligned columns (20). Dirichlet mixture file. Deletion pseudocount (0.1). No-deletion pseudocount (2.0). Insertion pseudocount (0.02). No-insertion pseudocount (1.0). Weight for generic versus sequence-set-specific residue abundances (1e+99). Initial temperature (1.2). Cooling factor per n iterations (1.44). Temperature lower bound (0.1). Print progress information at each iteration. Column-sampling moves per site-sampling move (1.0). Site sampling algorithm: 0=FAST 1=SLOW 2=FFT (0). Seed for pseudo-random numbers (1). SEE ALSO glam2format 1 , glam2mask 1 , glam2-purge 1 , glam2scan 1 The full Hypertext documentation of GLAM2 is available online at http://bioinformatics.org.au/glam2/ or on this computer in /usr/share/doc/glam2/. REFERENCE If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press). debian/glam2-purge.1.xml0000644000000000000000000001410211736403523012173 0ustar ]> &dhtitle; &dhproduct; &dhrelease; Andrew F Neuwald Author of purge, renamed glam2-purge in Debian. Martin C Frith Modified purge to be ANSI standard C and improved the user interface. Timothy L Bailey Modified purge to be ANSI standard C and improved the user interface. &dhfirstname; &dhsurname; Formatted this manpage in DocBook XML for the Debian distribution.
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The source code and the documentation of Purge and GLAM2 are released in the public domain. &dhucpackage; &dhsection; &dhpackage; Removes redundant sequences from a FASTA file &dhpackage; file DESCRIPTION glam2-purge is a modified version of Andrew Neuwald's purge program that removes redundant sequences from a FASTA file. This is recommended in order to prevent highly similar sequences distorting the search for motifs. Purge works with either DNA or protein sequences and creates an output file such that no two sequences have a (gapless) local alignment score greater than a threshold specified by the user. The output file is named <file>.<score>. The alignment score is based on the BLOSUM62 matrix for proteins, and on a +5/-1 scoring scheme for DNA. Purge can also be used to mask tandem repeats. It uses the XNU program for this purpose. OPTIONS Sequences are DNA (default: protein). Use blast heuristic method (default for protein). Use an exhaustive method (default for DNA). Keep first sequence in the set. Use xnu to mask protein tandem repeats. SEE ALSO glam2 1 , glam2format 1 , glam2mask 1 , glam2scan 1 , xnu 1 The full Hypertext documentation of GLAM2 is available online at http://bioinformatics.org.au/glam2/ or on this computer in /usr/share/doc/glam2/. REFERENCES Purge was written by Andy Neuwald and is described in more detail in Neuwald et al., "Gibbs motif sampling: detection of bacterial outer membrane protein repeats", Protein Science, 4:1618–1632, 1995. Please cite it if you use Purge. If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press). debian/glam2mask.10000644000000000000000000000354611736403523011142 0ustar .\" Title: GLAM2MASK .\" Author: Martin Frith .\" Generator: DocBook XSL Stylesheets v1.73.2 .\" Date: 05/19/2008 .\" Manual: glam2 Manual .\" Source: GLAM2 1056 .\" .TH "GLAM2MASK" "1" "05/19/2008" "GLAM2 1056" "glam2 Manual" .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .SH "NAME" glam2mask \- masks a GLAM2 motif in sequences .SH "SYNOPSIS" .HP 10 \fBglam2mask\fR [\fBoptions\fR] \fImy_motif\&.glam2\fR \fImy_seqs\&.fa\fR .SH "DESCRIPTION" .PP \fBglam2mask\fR masks a \fBglam2\fR motif out of sequences, so that weaker motifs can be found\&. Masking replaces residues aligned to key positions with the symbol \'x\'\&. By alternately applying \fBglam2\fR and \fBglam2mask\fR several times, it is possible to find the strongest, second\-strongest, third\-strongest, etc\&. motifs in a set of sequences\&. .SH "OPTIONS (DEFAULT SETTINGS)" .PP \fB\-o\fR .RS 4 Output file (\fIstdout\fR)\&. .RE .PP \fB\-x\fR .RS 4 Mask character (\fIx\fR)\&. .RE .SH "SEE ALSO" .PP \fBglam2format\fR(1), \fBglam2\fR(1), \fBglam2-purge\fR(1), \fBglam2scan\fR(1) .PP The full Hypertext documentation of GLAM2 is available online at \fIhttp://bioinformatics\&.org\&.au/glam2/\fR or on this computer in \fI/usr/share/doc/glam2/\fR\&. .SH "REFERENCE" .PP If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press)\&. .SH "AUTHORS" .PP \fBMartin Frith\fR .sp -1n .IP "" 4 Author of GLAM2\&. .PP \fBTimothy Bailey\fR .sp -1n .IP "" 4 Author of GLAM2\&. .PP \fBCharles Plessy\fR <\&plessy@debian\&.org\&> .sp -1n .IP "" 4 Formatted this manpage in DocBook XML for the Debian distribution\&. .SH "COPYRIGHT" .PP The source code and the documentation of GLAM2 are released in the public domain\&. .sp debian/glam2.10000644000000000000000000000654311736403523010266 0ustar .\" Title: GLAM2 .\" Author: Martin Frith .\" Generator: DocBook XSL Stylesheets v1.73.2 .\" Date: 05/19/2008 .\" Manual: glam2 Manual .\" Source: GLAM2 1056 .\" .TH "GLAM2" "1" "05/19/2008" "GLAM2 1056" "glam2 Manual" .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .SH "NAME" glam2 \- Gapped Local Alignment of Motifs .SH "SYNOPSIS" .HP 6 \fBglam2\fR [\fBoptions\fR] \fBalphabet\fR \fImy_seqs\&.fa\fR .PP An alphabet other than \fIp\fR or \fIn\fR is interpreted as the name of an alphabet file\&. .SH "DESCRIPTION" .PP GLAM2 is a software package for finding motifs in sequences, typically amino\-acid or nucleotide sequences\&. A motif is a re\-occurring sequence pattern: typical examples are the TATA box and the CAAX prenylation motif\&. The main innovation of GLAM2 is that it allows insertions and deletions in motifs\&. .SH "OPTIONS (DEFAULT SETTINGS)" .PP \fB\-h\fR .RS 4 Show all options and their default settings\&. .RE .PP \fB\-o\fR .RS 4 Output file (\fIstdout\fR)\&. .RE .PP \fB\-r\fR .RS 4 Number of alignment runs (\fI10\fR)\&. .RE .PP \fB\-n\fR .RS 4 End each run after this many iterations without improvement (\fI10000\fR)\&. .RE .PP \fB\-2\fR .RS 4 Examine both strands \- forward and reverse complement\&. .RE .PP \fB\-z\fR .RS 4 Minimum number of sequences in the alignment (\fI2\fR)\&. .RE .PP \fB\-a\fR .RS 4 Minimum number of aligned columns (\fI2\fR)\&. .RE .PP \fB\-b\fR .RS 4 Maximum number of aligned columns (\fI50\fR)\&. .RE .PP \fB\-w\fR .RS 4 Initial number of aligned columns (\fI20\fR)\&. .RE .PP \fB\-d\fR .RS 4 Dirichlet mixture file\&. .RE .PP \fB\-D\fR .RS 4 Deletion pseudocount (\fI0\&.1\fR)\&. .RE .PP \fB\-E\fR .RS 4 No\-deletion pseudocount (\fI2\&.0\fR)\&. .RE .PP \fB\-I\fR .RS 4 Insertion pseudocount (\fI0\&.02\fR)\&. .RE .PP \fB\-J\fR .RS 4 No\-insertion pseudocount (\fI1\&.0\fR)\&. .RE .PP \fB\-q\fR .RS 4 Weight for generic versus sequence\-set\-specific residue abundances (\fI1e+99\fR)\&. .RE .PP \fB\-t\fR .RS 4 Initial temperature (\fI1\&.2\fR)\&. .RE .PP \fB\-c\fR .RS 4 Cooling factor per n iterations (\fI1\&.44\fR)\&. .RE .PP \fB\-u\fR .RS 4 Temperature lower bound (\fI0\&.1\fR)\&. .RE .PP \fB\-p\fR .RS 4 Print progress information at each iteration\&. .RE .PP \fB\-m\fR .RS 4 Column\-sampling moves per site\-sampling move (\fI1\&.0\fR)\&. .RE .PP \fB\-x\fR .RS 4 Site sampling algorithm: \fI0\fR=FAST \fI1\fR=SLOW \fI2\fR=FFT (\fI0\fR)\&. .RE .PP \fB\-s\fR .RS 4 Seed for pseudo\-random numbers (\fI1\fR)\&. .RE .SH "SEE ALSO" .PP \fBglam2format\fR(1), \fBglam2mask\fR(1), \fBglam2-purge\fR(1), \fBglam2scan\fR(1) .PP The full Hypertext documentation of GLAM2 is available online at \fIhttp://bioinformatics\&.org\&.au/glam2/\fR or on this computer in \fI/usr/share/doc/glam2/\fR\&. .SH "REFERENCE" .PP If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press)\&. .SH "AUTHORS" .PP \fBMartin Frith\fR .sp -1n .IP "" 4 Author of GLAM2\&. .PP \fBTimothy Bailey\fR .sp -1n .IP "" 4 Author of GLAM2\&. .PP \fBCharles Plessy\fR <\&plessy@debian\&.org\&> .sp -1n .IP "" 4 Formatted this manpage in DocBook XML for the Debian distribution\&. .SH "COPYRIGHT" .PP The source code and the documentation of GLAM2 are released in the public domain\&. .sp debian/glam2.doc-base.manual0000644000000000000000000000071611736403523013053 0ustar Document: glam2-manual Title: GLAM2 Manual Author: Martin Frith, Timothy L Bailey Abstract: This manal covers the installation and usage of GLAM2. It provides a tutorial and a reference for the `glam2' program, a manual for the `glam2scan', `glam2format', `glam2mask' and `purge', as well as explanations about alphabets and Dirichlet mixtures. Section: Science/Biology Format: HTML Index: /usr/share/doc/glam2/index.html Files: /usr/share/doc/glam2/*.html debian/glam2.doc-base.method0000644000000000000000000000034711736403523013056 0ustar Document: glam2-method Title: GLAM2 Methods Author: Martin C Frith Section: Science/Biology Abstract: This manual explains in detail the statistical methods used in GLAM2. Format: PDF Files: /usr/share/doc/glam2/GLAM2_method.pdf debian/glam2format.1.xml0000644000000000000000000001304111736403523012265 0ustar ]> &dhtitle; &dhproduct; &dhrelease; Martin C Frith Author of GLAM2. Timothy L Bailey Author of GLAM2. &dhfirstname; &dhsurname; Formatted this manpage in DocBook XML for the Debian distribution.
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The source code and the documentation of GLAM2 are released in the public domain. &dhucpackage; &dhsection; &dhpackage; converts GLAM2 motifs to FASTA or MSF format &dhpackage; my_motif.glam2 Formats: fasta, msf. DESCRIPTION &dhpackage; reads in a motif found by glam2, and writes it in a standard alignment format (FASTA-with-gaps or MSF). This enables the alignment to be passed to third-party software, including graphical visualization tools such as Kalignvu, Boxshade, and WebLogo. On the other hand, not all the motif information is preserved: in particular, the key positions are lost. Only the top motif in glam2 output is converted. OPTIONS (default settings) Output file (stdout). Make a compact alignment. By default, residues that are inserted between key positions are written as unaligned with each other. This best reflects glam2's intention, but it can make the alignment large and full of gaps. With -c, inserted residues are written as arbitrarily aligned with each other, just as they appear in the glam2 output. Sequence file to make a global alignment by adding flanking sequences from the original FASTA-format sequence file. The flanking sequences will be written as either unaligned with each other or arbitrarily aligned, depending on the -c option. The sequences should have unique names and their order should be unchanged. SEE ALSO boxshade 1, glam2 1 , glam2mask 1 , glam2-purge 1 , glam2scan 1 The full Hypertext documentation of GLAM2 is available online at http://bioinformatics.org.au/glam2/ or on this computer in /usr/share/doc/glam2/. REFERENCE If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press). debian/rules0000755000000000000000000000147312241430631010247 0ustar #!/usr/bin/make -f DEBPKGNAME := $(shell dpkg-parsechangelog | awk '/^Source:/ {print $$2}') BINDIR = $(CURDIR)/debian/$(DEBPKGNAME)/usr/bin SRCDIR=src %: dh $@ --sourcedirectory=$(SRCDIR) --parallel override_dh_auto_build: dh_auto_build make --directory=$(SRCDIR) glam2fft make --directory=purge override_dh_compress: dh_compress --exclude=.pdf override_dh_install: dh_install # purge is renamed glam2-purge to avoid namespace problems. mv $(BINDIR)/purge $(BINDIR)/glam2-purge # FFT is enabled by default in Debian. mv $(BINDIR)/glam2fft $(BINDIR)/glam2 override_dh_clean: dh_clean rm -f purge/*.o purge/purge src/*.o src/glam2 src/glam2mask scr/glam2format src/glam2scan src/glam2fft src/glam2format get-orig-source: mkdir -p ../tarballs uscan --verbose --force-download --repack --destdir=../tarballs debian/manpages0000644000000000000000000000013711736403523010711 0ustar debian/glam2.1 debian/glam2format.1 debian/glam2mask.1 debian/glam2-purge.1 debian/glam2scan.1 debian/examples0000644000000000000000000000001311736403523010725 0ustar examples/* debian/watch0000644000000000000000000000011011736403523010213 0ustar version=3 http://bioinformatics.org.au/glam2/archive/glam2-(\d+)\.zip debian/upstream0000644000000000000000000000117312214301042010740 0ustar Contact: Martin C Frith and Timothy L Bailey Homepage: http://bioinformatics.org.au/glam2/ Name: GLAM2 Reference: author: Frith, Martin C. AND Saunders, Neil F. W. AND Kobe, Bostjan AND Bailey, Timothy L. journal: PLoS Computational Biology publisher: Public Library of Science title: Discovering Sequence Motifs with Arbitrary Insertions and Deletions year: 2008 month: 05 volume: 4 DOI: 10.1371/journal.pcbi.1000071 PMID: 18437229 url: http://dx.plos.org/10.1371/journal.pcbi.1000071 pages: e1000071 number: 5 Watch: http://bioinformatics.org.au/glam2/archive/glam2-(\d+)\.zip debian/copyright0000644000000000000000000000624012241430222011113 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Contact: Martin C Frith Timothy L Bailey Source: http://bioinformatics.org.au/glam2/archive/glam2-1064.zip Glam2 is now included into the MEME software suite and not maintained separately at this place any more. Since MEME is non-free we are keeping this old version of glam2 in Debian. Se also https://lists.debian.org/debian-med/2013/11/msg00034.html Files: * Copyright: 2007 Martin C Frith 2007 Timothy L Bailey License: PD_glam GLAM2 was developed by Martin C Frith, working at the Computational Biology Research Center in Tokyo, and Timothy L Bailey, working at the Institute for Molecular Bioscience in Brisbane. The source code and documentation are hereby released into the public domain. If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (PLoS Comput Biol. 2008 Apr 25;4(4):e1000071.). Files: purge/* Copyright: Andrew Neuwald License: PD_ncbi PUBLIC DOMAIN NOTICE National Center for Biotechnology Information . This software/database is a "United States Government Work" under the terms of the United States Copyright Act. It was written as part of the author's official duties as a United States Government employee and thus cannot be copyrighted. This software is freely available to the public for use. The National Library of Medicine and the U.S. Government have not placed any restriction on its use or reproduction. . Although reasonable efforts have been taken to ensure the accuracy and reliability of the software and data, the NLM and the U.S. Government do not and cannot warrant the performance or results that may be obtained by using this software or data. The NLM and the U.S. Government disclaim all warranties, express or implied, including warranties of performance, merchantability or fitness for any particular purpose. . Please cite . Neuwald, Liu, & Lawrence (1995) "Gibbs motif sampling: detection of bacterial outer membrane protein repeats" Protein Science 4, 1618-1632. (for Gibbs site sampling, Gibbs motif sampling, purge, and scan programs) . and . Lawrence, Altschul, Boguski, Liu, Neuwald & Wootton (1993) "Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment", Science 262:208-214. (for Gibbs site sampling program) . in any work or product based on this material. . The data structures used in this program are part of a package of C code for molecular biological applications being developed by A. F. Neuwald. Files: debian/* Copyright: 2007 Steffen Moeller 2007-2008 Charles Plessy 2011-2013 Andreas Tille License: PD The package is in the public domain and so shall then be the packaging for Debian of Steffen Moeller and Charles Plessy . debian/source/0000755000000000000000000000000012214301042010453 5ustar debian/source/format0000644000000000000000000000001412214301042011661 0ustar 3.0 (quilt) debian/README.Debian0000644000000000000000000000043711736403523011237 0ustar glam2 for Debian ---------------- We renamed purge glam2-purge, to avoid namespace collision. glam2 is compiled with -O2 optimisation level. Please contact us if you notice performance issues compared to -O3. -- Steffen Moeller Tue, 13 Nov 2007 00:35:50 +0100 debian/glam2scan.10000644000000000000000000000436311736403523011131 0ustar .\" Title: GLAM2SCAN .\" Author: Martin Frith .\" Generator: DocBook XSL Stylesheets v1.73.2 .\" Date: 05/19/2008 .\" Manual: glam2 Manual .\" Source: GLAM2 1056 .\" .TH "GLAM2SCAN" "1" "05/19/2008" "GLAM2 1056" "glam2 Manual" .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .SH "NAME" glam2scan \- finds a GLAM2 motif in a database .SH "SYNOPSIS" .HP 10 \fBglam2scan\fR [\fBoptions\fR] \fBalphabet\fR \fImy_motif\&.glam2\fR \fImy_seqs\&.fa\fR .PP An alphabet other than \fIp\fR or \fIn\fR is interpreted as the name of an alphabet file\&. .SH "DESCRIPTION" .PP \fBglam2scan\fR finds matches, in a sequence database, to a motif discovered by \fBglam2\fR\&. Each match receives a score, indicating how well it fits the motif\&. .SH "OPTIONS (DEFAULT SETTINGS)" .PP \fB\-h\fR .RS 4 Show all options and their default settings\&. .RE .PP \fB\-o\fR .RS 4 Output file (\fIstdout\fR)\&. .RE .PP \fB\-n\fR .RS 4 Number of alignments to report (\fI25\fR)\&. .RE .PP \fB\-2\fR .RS 4 Examine both strands \- forward and reverse complement\&. .RE .PP \fB\-D\fR .RS 4 Deletion pseudocount (\fI0\&.1\fR)\&. .RE .PP \fB\-E\fR .RS 4 No\-deletion pseudocount (\fI2\&.0\fR)\&. .RE .PP \fB\-I\fR .RS 4 Insertion pseudocount (\fI0\&.02\fR)\&. .RE .PP \fB\-J\fR .RS 4 No\-insertion pseudocount (\fI1\&.0\fR)\&. .RE .PP \fB\-d\fR .RS 4 Dirichlet mixture file\&. .RE .SH "SEE ALSO" .PP \fBglam2format\fR(1), \fBglam2mask\fR(1), \fBglam2-purge\fR(1), \fBglam2\fR(1) .PP The full Hypertext documentation of GLAM2 is available online at \fIhttp://bioinformatics\&.org\&.au/glam2/\fR or on this computer in \fI/usr/share/doc/glam2/\fR\&. .SH "REFERENCE" .PP If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press)\&. .SH "AUTHORS" .PP \fBMartin Frith\fR .sp -1n .IP "" 4 Author of GLAM2\&. .PP \fBTimothy Bailey\fR .sp -1n .IP "" 4 Author of GLAM2\&. .PP \fBCharles Plessy\fR <\&plessy@debian\&.org\&> .sp -1n .IP "" 4 Formatted this manpage in DocBook XML for the Debian distribution\&. .SH "COPYRIGHT" .PP The source code and the documentation of GLAM2 are released in the public domain\&. .sp debian/changelog0000644000000000000000000000324412241433512011040 0ustar glam2 (1064-3) unstable; urgency=low [ Charles Plessy ] * Documented information in ‘debian/upstream’. [ Andreas Tille ] * debian/upstream: Took over some bit sof information from tasks file and move DOI+PMID to references * debian/control: - canonical Vcs fields - cme fix dpkg-control * debian/source/format: 3.0 (quilt) * debhelper 9 (control+compat) * debian/copyright: DEP5 * debian/NEWS.Debian: Explain maintenance in MEME * debian/patches/hardening: propagate hardening options -- Andreas Tille Fri, 15 Nov 2013 15:07:59 +0100 glam2 (1064-2) unstable; urgency=low * debian/control, debian/reference: simplified long description and moved bibliographic references to a new file. -- Charles Plessy Tue, 21 Apr 2009 21:49:54 +0900 glam2 (1064-1) unstable; urgency=low [ Charles Plessy ] * New upstream release - One paragraph added to the tutorial. - Uses CFLAGS in makefiles (thanks Martin!) * Changed the doc-base section according to the new policy. * Updated my email address. * Added a get-orig-source target in debian/rules. * debian/patches/Makefiles removed because obsoleted. [ Andreas Tille ] * Better formatting of long description. -- Charles Plessy Mon, 19 May 2008 18:46:20 +0900 glam2 (1058-1) unstable; urgency=low * New upstream release (Fixes bug in usage message: z_def was out of order.) -- Charles Plessy Thu, 14 Feb 2008 13:05:54 +0900 glam2 (1056-1) unstable; urgency=low * Initial release (Closes: #45237) -- Steffen Moeller Tue, 13 Nov 2007 00:35:50 +0100 debian/patches/0000755000000000000000000000000012241433276010621 5ustar debian/patches/hardening.patch0000644000000000000000000000337712241433276013613 0ustar Author: Andreas Tille LastChanged: Fri, 15 Nov 2013 15:07:59 +0100 Description: propagate hardening options --- a/src/Makefile +++ b/src/Makefile @@ -24,32 +24,32 @@ FSRC = glam2format.c alignment.c fasta.c MSRC = glam2mask.c alignment.c fasta.c util.c # Compiler options: -CFLAGS = -Wall -O3 +CFLAGS += -Wall -O3 # Default action: compile glam2, glam2scan, glam2format, and glam2mask all: glam2 glam2scan glam2format glam2mask # Command for compiling glam2: glam2: $(GSRC) *.h Makefile - cc $(CFLAGS) -o glam2 $(GSRC) -lm + cc $(CFLAGS) -o glam2 $(GSRC) -lm $(LDFLAGS) # Command for compiling glam2scan: glam2scan: $(SSRC) *.h Makefile - cc $(CFLAGS) -o glam2scan $(SSRC) -lm + cc $(CFLAGS) -o glam2scan $(SSRC) -lm $(LDFLAGS) # Command for compiling glam2format: glam2format: $(FSRC) *.h Makefile - cc $(CFLAGS) -o glam2format $(FSRC) -lm + cc $(CFLAGS) -o glam2format $(FSRC) -lm $(LDFLAGS) # Command for compiling glam2mask: glam2mask: $(MSRC) *.h Makefile - cc $(CFLAGS) -o glam2mask $(MSRC) -lm + cc $(CFLAGS) -o glam2mask $(MSRC) -lm $(LDFLAGS) # Here follow commands for compiling special versions of the programs # Compile glam2 including FFT algorithm (requires FFTW to be installed): glam2fft: $(GSRC) convolve.c *.h Makefile - cc $(CFLAGS) -DFFT -o glam2fft $(GSRC) convolve.c -lm -lfftw3 + cc $(CFLAGS) -DFFT -o glam2fft $(GSRC) convolve.c -lm -lfftw3 $(LDFLAGS) # Compile for debugging with gdb or valgrind, with extra compiler warnings: glam2_d: $(GSRC) *.h Makefile --- a/purge/Makefile +++ b/purge/Makefile @@ -1,6 +1,6 @@ # Compiler options: -CFLAGS = -Wall -O3 +CFLAGS += -Wall -O3 # Command for compiling purge: purge: *.c *.h Makefile - cc $(CFLAGS) -o purge *.c -lm + cc $(CFLAGS) -o purge *.c -lm $(LDFLAGS) debian/patches/series0000644000000000000000000000002012241433032012014 0ustar hardening.patch debian/compat0000644000000000000000000000000212241425161010362 0ustar 9 debian/glam2mask.1.xml0000644000000000000000000001111311736403523011726 0ustar ]> &dhtitle; &dhproduct; &dhrelease; Martin C Frith Author of GLAM2. Timothy L Bailey Author of GLAM2. &dhfirstname; &dhsurname; Formatted this manpage in DocBook XML for the Debian distribution.
&dhemail;
The source code and the documentation of GLAM2 are released in the public domain. &dhucpackage; &dhsection; &dhpackage; masks a GLAM2 motif in sequences &dhpackage; my_motif.glam2 my_seqs.fa DESCRIPTION &dhpackage; masks a glam2 motif out of sequences, so that weaker motifs can be found. Masking replaces residues aligned to key positions with the symbol 'x'. By alternately applying glam2 and glam2mask several times, it is possible to find the strongest, second-strongest, third-strongest, etc. motifs in a set of sequences. OPTIONS (default settings) Output file (stdout). Mask character (x). SEE ALSO glam2format 1 , glam2 1 , glam2-purge 1 , glam2scan 1 The full Hypertext documentation of GLAM2 is available online at http://bioinformatics.org.au/glam2/ or on this computer in /usr/share/doc/glam2/. REFERENCE If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press). debian/docs0000644000000000000000000000004611736403523010045 0ustar README doc/*.html doc/*.css doc/*.pdf debian/glam2scan.1.xml0000644000000000000000000001340411736403523011724 0ustar ]> &dhtitle; &dhproduct; &dhrelease; Martin C Frith Author of GLAM2. Timothy L Bailey Author of GLAM2. &dhfirstname; &dhsurname; Formatted this manpage in DocBook XML for the Debian distribution.
&dhemail;
The source code and the documentation of GLAM2 are released in the public domain. &dhucpackage; &dhsection; &dhpackage; finds a GLAM2 motif in a database &dhpackage; my_motif.glam2 my_seqs.fa An alphabet other than p or n is interpreted as the name of an alphabet file. DESCRIPTION glam2scan finds matches, in a sequence database, to a motif discovered by glam2. Each match receives a score, indicating how well it fits the motif. OPTIONS (default settings) Show all options and their default settings. Output file (stdout). Number of alignments to report (25). Examine both strands - forward and reverse complement. Deletion pseudocount (0.1). No-deletion pseudocount (2.0). Insertion pseudocount (0.02). No-insertion pseudocount (1.0). Dirichlet mixture file. SEE ALSO glam2format 1 , glam2mask 1 , glam2-purge 1 , glam2 1 The full Hypertext documentation of GLAM2 is available online at http://bioinformatics.org.au/glam2/ or on this computer in /usr/share/doc/glam2/. REFERENCE If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press). debian/glam2-purge.10000644000000000000000000000551511736403523011404 0ustar .\" Title: GLAM2-PURGE .\" Author: Andrew Neuwald .\" Generator: DocBook XSL Stylesheets v1.73.2 .\" Date: 05/19/2008 .\" Manual: glam2 Manual .\" Source: GLAM2 1056 .\" .TH "GLAM2\-PURGE" "1" "05/19/2008" "GLAM2 1056" "glam2 Manual" .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .SH "NAME" glam2-purge \- Removes redundant sequences from a FASTA file .SH "SYNOPSIS" .HP 12 \fBglam2\-purge\fR \fIfile\fR \fBscore\fR [\fBoptions\fR] .SH "DESCRIPTION" .PP \fBglam2\-purge\fR is a modified version of Andrew Neuwald\'s \fBpurge\fR program that removes redundant sequences from a FASTA file\&. This is recommended in order to prevent highly similar sequences distorting the search for motifs\&. Purge works with either DNA or protein sequences and creates an output file such that no two sequences have a (gapless) local alignment score greater than a threshold specified by the user\&. The output file is named \&.\&. The alignment score is based on the BLOSUM62 matrix for proteins, and on a +5/\-1 scoring scheme for DNA\&. Purge can also be used to mask tandem repeats\&. It uses the XNU program for this purpose\&. .SH "OPTIONS" .PP \fB\-n\fR .RS 4 Sequences are DNA (default: protein)\&. .RE .PP \fB\-b\fR .RS 4 Use blast heuristic method (default for protein)\&. .RE .PP \fB\-e\fR .RS 4 Use an exhaustive method (default for DNA)\&. .RE .PP \fB\-q\fR .RS 4 Keep first sequence in the set\&. .RE .PP \fB\-x\fR .RS 4 Use xnu to mask protein tandem repeats\&. .RE .SH "SEE ALSO" .PP \fBglam2\fR(1), \fBglam2format\fR(1), \fBglam2mask\fR(1), \fBglam2scan\fR(1), \fBxnu\fR(1) .PP The full Hypertext documentation of GLAM2 is available online at \fIhttp://bioinformatics\&.org\&.au/glam2/\fR or on this computer in \fI/usr/share/doc/glam2/\fR\&. .SH "REFERENCES" .PP Purge was written by Andy Neuwald and is described in more detail in Neuwald et al\&., "Gibbs motif sampling: detection of bacterial outer membrane protein repeats", Protein Science, 4:1618\(en1632, 1995\&. Please cite it if you use Purge\&. .PP If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press)\&. .SH "AUTHORS" .PP \fBAndrew Neuwald\fR .sp -1n .IP "" 4 Author of purge, renamed glam2\-purge in Debian\&. .PP \fBMartin Frith\fR .sp -1n .IP "" 4 Modified purge to be ANSI standard C and improved the user interface\&. .PP \fBTimothy Bailey\fR .sp -1n .IP "" 4 Modified purge to be ANSI standard C and improved the user interface\&. .PP \fBCharles Plessy\fR <\&plessy@debian\&.org\&> .sp -1n .IP "" 4 Formatted this manpage in DocBook XML for the Debian distribution\&. .SH "COPYRIGHT" .PP The source code and the documentation of Purge and GLAM2 are released in the public domain\&. .sp debian/glam2format.10000644000000000000000000000527411736403523011477 0ustar .\" Title: GLAM2FORMAT .\" Author: Martin Frith .\" Generator: DocBook XSL Stylesheets v1.73.2 .\" Date: 05/19/2008 .\" Manual: glam2 Manual .\" Source: GLAM2 1056 .\" .TH "GLAM2FORMAT" "1" "05/19/2008" "GLAM2 1056" "glam2 Manual" .\" disable hyphenation .nh .\" disable justification (adjust text to left margin only) .ad l .SH "NAME" glam2format \- converts GLAM2 motifs to FASTA or MSF format .SH "SYNOPSIS" .HP 12 \fBglam2format\fR [\fBoptions\fR] \fBmy_format\fR \fImy_motif\&.glam2\fR .PP Formats: fasta, msf\&. .SH "DESCRIPTION" .PP \fBglam2format\fR reads in a motif found by \fBglam2\fR, and writes it in a standard alignment format (FASTA\-with\-gaps or MSF)\&. This enables the alignment to be passed to third\-party software, including graphical visualization tools such as Kalignvu, Boxshade, and WebLogo\&. On the other hand, not all the motif information is preserved: in particular, the key positions are lost\&. Only the top motif in \fBglam2\fR output is converted\&. .SH "OPTIONS (DEFAULT SETTINGS)" .PP \fB\-o\fR .RS 4 Output file (\fIstdout\fR)\&. .RE .PP \fB\-c\fR .RS 4 Make a compact alignment\&. By default, residues that are inserted between key positions are written as unaligned with each other\&. This best reflects \fBglam2\fR\'s intention, but it can make the alignment large and full of gaps\&. With \fI\-c\fR, inserted residues are written as arbitrarily aligned with each other, just as they appear in the \fBglam2\fR output\&. .RE .PP \fB\-f\fR .RS 4 Sequence file to make a \(lqglobal\(rq alignment by adding flanking sequences from the original FASTA\-format sequence file\&. The flanking sequences will be written as either unaligned with each other or arbitrarily aligned, depending on the \fI\-c\fR option\&. The sequences should have unique names and their order should be unchanged\&. .RE .SH "SEE ALSO" .PP \fBboxshade\fR(1), \fBglam2\fR(1), \fBglam2mask\fR(1), \fBglam2-purge\fR(1), \fBglam2scan\fR(1) .PP The full Hypertext documentation of GLAM2 is available online at \fIhttp://bioinformatics\&.org\&.au/glam2/\fR or on this computer in \fI/usr/share/doc/glam2/\fR\&. .SH "REFERENCE" .PP If you use GLAM2, please cite: MC Frith, NFW Saunders, B Kobe, TL Bailey (2008) Discovering sequence motifs with arbitrary insertions and deletions, PLoS Computational Biology (in press)\&. .SH "AUTHORS" .PP \fBMartin Frith\fR .sp -1n .IP "" 4 Author of GLAM2\&. .PP \fBTimothy Bailey\fR .sp -1n .IP "" 4 Author of GLAM2\&. .PP \fBCharles Plessy\fR <\&plessy@debian\&.org\&> .sp -1n .IP "" 4 Formatted this manpage in DocBook XML for the Debian distribution\&. .SH "COPYRIGHT" .PP The source code and the documentation of GLAM2 are released in the public domain\&. .sp