./PaxHeaders.8289/aragorn1.2.36 0000644 0001750 0000144 00000000131 12114676617 014226 x ustar 00 0000000 0000000 30 mtime=1362328975.349346101
29 atime=1362328995.67675618
30 ctime=1362328975.349346101
aragorn1.2.36/ 0000755 0001750 0000144 00000000000 12114676617 013523 5 ustar 00bjorn users 0000000 0000000 aragorn1.2.36/PaxHeaders.8289/aragorn.1 0000644 0001750 0000144 00000000132 12114675742 015660 x ustar 00 0000000 0000000 30 mtime=1362328546.047621599
30 atime=1362328677.632281439
30 ctime=1362328975.349346101
aragorn1.2.36/aragorn.1 0000644 0001750 0000144 00000021615 12114675742 015241 0 ustar 00bjorn users 0000000 0000000 '\" t
.\" Title: aragorn
.\" Author: [see the "AUTHORS" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1
.\" Date: 02/24/2013
.\" Manual: \ \&
.\" Source: \ \&
.\" Language: English
.\"
.TH "ARAGORN" "1" "02/24/2013" "\ \&" "\ \&"
.\" -----------------------------------------------------------------
.\" * Define some portability stuff
.\" -----------------------------------------------------------------
.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.\" http://bugs.debian.org/507673
.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.ie \n(.g .ds Aq \(aq
.el .ds Aq '
.\" -----------------------------------------------------------------
.\" * set default formatting
.\" -----------------------------------------------------------------
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.\" -----------------------------------------------------------------
.\" * MAIN CONTENT STARTS HERE *
.\" -----------------------------------------------------------------
.SH "NAME"
aragorn \- detect tRNA genes in nucleotide sequences
.SH "SYNOPSIS"
.sp
\fBaragorn\fR [\fIOPTION\fR]\&... \fIFILE\fR
.SH "OPTIONS"
.PP
\fB\-m\fR
.RS 4
Search for tmRNA genes\&.
.RE
.PP
\fB\-t\fR
.RS 4
Search for tRNA genes\&. By default, all are detected\&. If one of
\fB\-m\fR
or
\fB\-t\fR
is specified, then the other is not detected unless specified as well\&.
.RE
.PP
\fB\-mt\fR
.RS 4
Search for Metazoan mitochondrial tRNA genes\&. tRNA genes with introns not detected\&.
\fB\-i\fR,
\fB\-sr\fR
switchs ignored\&. Composite Metazoan mitochondrial genetic code used\&.
.RE
.PP
\fB\-mtmam\fR
.RS 4
Search for Mammalian mitochondrial tRNA genes\&.
\fB\-i\fR,
\fB\-sr\fR
switchs ignored\&.
\fB\-tv\fR
switch set\&. Mammalian mitochondrial genetic code used\&.
.RE
.PP
\fB\-mtx\fR
.RS 4
Same as
\fB\-mt\fR
but low scoring tRNA genes are not reported\&.
.RE
.PP
\fB\-mtd\fR
.RS 4
Overlapping metazoan mitochondrial tRNA genes on opposite strands are reported\&.
.RE
.PP
\fB\-gc\fR[\fInum\fR]
.RS 4
Use the GenBank transl_table = [\fInum\fR] genetic code\&. Individual modifications can be appended using
\fI,BBB\fR= B = A,C,G, or T\&. is the three letter code for an amino\-acid\&. More than one modification can be specified\&. eg
\fB\-gcvert\fR,aga=Trp,agg=Trp uses the Vertebrate Mitochondrial code and the codons AGA and AGG changed to Tryptophan\&.
.RE
.PP
\fB\-gcstd\fR
.RS 4
Use standard genetic code\&.
.RE
.PP
\fB\-gcmet\fR
.RS 4
Use composite Metazoan mitochondrial genetic code\&.
.RE
.PP
\fB\-gcvert\fR
.RS 4
Use Vertebrate mitochondrial genetic code\&.
.RE
.PP
\fB\-gcinvert\fR
.RS 4
Use Invertebrate mitochondrial genetic code\&.
.RE
.PP
\fB\-gcyeast\fR
.RS 4
Use Yeast mitochondrial genetic code\&.
.RE
.PP
\fB\-gcprot\fR
.RS 4
Use Mold/Protozoan/Coelenterate mitochondrial genetic code\&.
.RE
.PP
\fB\-gcciliate\fR
.RS 4
Use Ciliate genetic code\&.
.RE
.PP
\fB\-gcflatworm\fR
.RS 4
Use Echinoderm/Flatworm mitochondrial genetic code
.RE
.PP
\fB\-gceuplot\fR
.RS 4
Use Euplotid genetic code\&.
.RE
.PP
\fB\-gcbact\fR
.RS 4
Use Bacterial/Plant Chloroplast genetic code\&.
.RE
.PP
\fB\-gcaltyeast\fR
.RS 4
Use alternative Yeast genetic code\&.
.RE
.PP
\fB\-gcascid\fR
.RS 4
Use Ascidian Mitochondrial genetic code\&.
.RE
.PP
\fB\-gcaltflat\fR
.RS 4
Use alternative Flatworm Mitochondrial genetic code\&.
.RE
.PP
\fB\-gcblep\fR
.RS 4
Use Blepharisma genetic code\&.
.RE
.PP
\fB\-gcchloroph\fR
.RS 4
Use Chlorophycean Mitochondrial genetic code\&.
.RE
.PP
\fB\-gctrem\fR
.RS 4
Use Trematode Mitochondrial genetic code\&.
.RE
.PP
\fB\-gcscen\fR
.RS 4
Use Scenedesmus obliquus Mitochondrial genetic code\&.
.RE
.PP
\fB\-gcthraust\fR
.RS 4
Use Thraustochytrium Mitochondrial genetic code\&.
.RE
.PP
\fB\-tv\fR
.RS 4
Do not search for mitochondrial TV replacement loop tRNA genes\&. Only relevant if
\fB\-mt\fR
used\&.
.RE
.PP
\fB\-c7\fR
.RS 4
Search for tRNA genes with 7 base C\-loops only\&.
.RE
.PP
\fB\-i\fR
.RS 4
Search for tRNA genes with introns in anticodon loop with maximum length 3000 bases\&. Minimum intron length is 0 bases\&. Ignored if
\fB\-m\fR
is specified\&.
.RE
.PP
\fB\-i\fR[\fImax\fR]
.RS 4
Search for tRNA genes with introns in anticodon loop with maximum length [\fImax\fR] bases\&. Minimum intron length is 0 bases\&. Ignored if
\fB\-m\fR
is specified\&.
.RE
.PP
\fB\-i\fR[\fImin\fR],[\fImax\fR]
.RS 4
Search for tRNA genes with introns in anticodon loop with maximum length [\fImax\fR] bases, and minimum length [\fImin\fR] bases\&. Ignored if
\fB\-m\fR
is specified\&.
.RE
.PP
\fB\-io\fR
.RS 4
Same as
\fB\-i\fR, but allow tRNA genes with long introns to overlap shorter tRNA genes\&.
.RE
.PP
\fB\-if\fR
.RS 4
Same as
\fB\-i\fR, but fix intron between positions 37 and 38 on C\-loop (one base after anticodon)\&.
.RE
.PP
\fB\-ifo\fR
.RS 4
Same as
\fB\-if\fR
and
\fB\-io\fR
combined\&.
.RE
.PP
\fB\-ir\fR
.RS 4
Same as
\fB\-i\fR, but report tRNA genes with minimum length [\fImin\fR] bases rather than search for tRNA genes with minimum length [\fImin\fR] bases\&. With this switch, [\fImin\fR] acts as an output filter, minimum intron length for searching is still 0 bases\&.
.RE
.PP
\fB\-c\fR
.RS 4
Assume that each sequence has a circular topology\&. Search wraps around each end\&. Default setting\&.
.RE
.PP
\fB\-l\fR
.RS 4
Assume that each sequence has a linear topology\&. Search does not wrap\&.
.RE
.PP
\fB\-d\fR
.RS 4
Double\&. Search both strands of each sequence\&. Default setting\&.
.RE
.PP
\fB\-s\fR or \fB\-s+\fR
.RS 4
Single\&. Do not search the complementary (antisense) strand of each sequence\&.
.RE
.PP
\fB\-sc\fR or \fB\-s\-\fR
.RS 4
Single complementary\&. Do not search the sense strand of each sequence\&.
.RE
.PP
\fB\-ps\fR
.RS 4
Lower scoring thresholds to 95% of default levels\&.
.RE
.PP
\fB\-ps\fR[\fInum\fR]
.RS 4
Change scoring thresholds to [\fInum\fR] percent of default levels\&.
.RE
.PP
\fB\-rp\fR
.RS 4
Flag possible pseudogenes (score < 100 or tRNA anticodon loop <> 7 bases long)\&. Note that genes with score < 100 will not be detected or flagged if scoring thresholds are not also changed to below 100% (see \-ps switch)\&.
.RE
.PP
\fB\-seq\fR
.RS 4
Print out primary sequence\&.
.RE
.PP
\fB\-br\fR
.RS 4
Show secondary structure of tRNA gene primary sequence using round brackets\&.
.RE
.PP
\fB\-fasta\fR
.RS 4
Print out primary sequence in fasta format\&.
.RE
.PP
\fB\-fo\fR
.RS 4
Print out primary sequence in fasta format only (no secondary structure)\&.
.RE
.PP
\fB\-fon\fR
.RS 4
Same as
\fB\-fo\fR, with sequence and gene numbering in header\&.
.RE
.PP
\fB\-fos\fR
.RS 4
Same as
\fB\-fo\fR, with no spaces in header\&.
.RE
.PP
\fB\-fons\fR
.RS 4
Same as
\fB\-fo\fR, with sequence and gene numbering, but no spaces\&.
.RE
.PP
\fB\-w\fR
.RS 4
Print out in Batch mode\&.
.RE
.PP
\fB\-ss\fR
.RS 4
Use the stricter canonical 1\-2 bp spacer1 and 1 bp spacer2\&. Ignored if
\fB\-mt\fR
set\&. Default is to allow 3 bp spacer1 and 0\-2 bp spacer2, which may degrade selectivity\&.
.RE
.PP
\fB\-v\fR
.RS 4
Verbose\&. Prints out information during search to STDERR\&.
.RE
.PP
\fB\-a\fR
.RS 4
Print out tRNA domain for tmRNA genes\&.
.RE
.PP
\fB\-a7\fR
.RS 4
Restrict tRNA astem length to a maximum of 7 bases
.RE
.PP
\fB\-aa\fR
.RS 4
Display message if predicted iso\-acceptor species does not match species in sequence name (if present)\&.
.RE
.PP
\fB\-j\fR
.RS 4
Display 4\-base sequence on 3\*(Aq end of astem regardless of predicted amino\-acyl acceptor length\&.
.RE
.PP
\fB\-jr\fR
.RS 4
Allow some divergence of 3\*(Aq amino\-acyl acceptor sequence from NCCA\&.
.RE
.PP
\fB\-jr4\fR
.RS 4
Allow some divergence of 3\*(Aq amino\-acyl acceptor sequence from NCCA, and display 4 bases\&.
.RE
.PP
\fB\-q\fR
.RS 4
Dont print configuration line (which switchs and files were used)\&.
.RE
.PP
\fB\-rn\fR
.RS 4
Repeat sequence name before summary information\&.
.RE
.PP
\fB\-O\fR [\fIoutfile\fR]
.RS 4
Print output to
\fI\&. If [\*(Aqoutfile\fR] already exists, it is overwritten\&. By default all output goes to stdout\&.
.RE
.SH "DESCRIPTION"
.sp
aragorn detects tRNA, mtRNA, and tmRNA genes\&. A minimum requirement is at least a 32 bit compiler architecture (variable types int and unsigned int are at least 4 bytes long)\&.
.sp
[\fIFILE\fR] is assumed to contain one or more sequences in FASTA format\&. Results of the search are printed to STDOUT\&. All switches are optional and case\-insensitive\&. Unless \-i is specified, tRNA genes containing introns are not detected\&.
.SH "AUTHORS"
.sp
Bjorn Canback , Dean Laslett
.SH "REFERENCES"
.sp
Laslett, D\&. and Canback, B\&. (2004) ARAGORN, a program for the detection of transfer RNA and transfer\-messenger RNA genes in nucleotide sequences Nucleic Acids Research, 32;11\-16
.sp
Laslett, D\&. and Canback, B\&. (2008) ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences Bioinformatics, 24(2); 172\-175\&.
aragorn1.2.36/PaxHeaders.8289/aragorn1.2.36.c 0000644 0001750 0000144 00000000132 12112405740 016375 x ustar 00 0000000 0000000 30 mtime=1361710048.509875992
30 atime=1362131382.854138148
30 ctime=1362328975.349346101
aragorn1.2.36/aragorn1.2.36.c 0000644 0001750 0000144 00001312072 12112405740 015757 0 ustar 00bjorn users 0000000 0000000
/*
---------------------------------------------------------------
ARAGORN v1.2.36 Dean Laslett
---------------------------------------------------------------
ARAGORN (together with ARWEN at last)
Detects tRNA, mtRNA, and tmRNA genes in nucleotide sequences
Copyright (C) 2003-2015 Dean Laslett
Please, report bugs and suggestions of improvements to the authors
E-mail: Björn Canbäck: bcanback@acgt.se
Dean Laslett: gaiaquark@gmail.com
Version 1.2.36 February 15th, 2013.
Thanks to Sascha Steinbiss for fixing more bugs
Please reference the following papers if you use this
program as part of any published research.
Laslett, D. and Canback, B. (2004)
ARAGORN, a program for the detection of transfer RNA and
transfer-messenger RNA genes in nucleotide sequences.
Nucleic Acids Research, 32;11-16.
Laslett, D. and Canback, B. (2008)
ARWEN: a program to detect tRNA genes in
metazoan mitochondrial nucleotide sequences.
Bioinformatics, 24(2); 172-175.
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; version 2 of the License, (see below).
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.
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END OF TERMS AND CONDITIONS
*/
/*
---------------------------------------------------------------
ARAGORN v1.2.36 Dean Laslett
---------------------------------------------------------------
aragorn detects tRNA, mtRNA, and tmRNA genes.
A minimum requirement is at least a 32 bit compiler architecture
(variable types int and unsigned int are at least 4 bytes long).
Usage:
aragorn -v -s -d -c -l -j -a -q -rn -w -ifro, -t -m -mt
-gc -tv -seq -br -fasta -fo -o
is assumed to contain one or more sequences
in FASTA format. Results of the search are printed to
STDOUT. All switches are optional and case-insensitive.
Unless -i is specified, tRNA genes containing introns
are not detected.
-m Search for tmRNA genes.
-t Search for tRNA genes.
By default, all are detected. If one of
-m or -t is specified, then the other
is not detected unless specified as well.
-mt Search for Metazoan mitochondrial tRNA genes.
tRNA genes with introns not detected. -i,-sr switchs
ignored. Composite Metazoan mitochondrial
genetic code used.
-mtmam Search for Mammalian mitochondrial tRNA
genes. -i,-sr switchs ignored. -tv switch set.
Mammalian mitochondrial genetic code used.
-mtx Same as -mt but low scoring tRNA genes are
not reported.
-mtd Overlapping metazoan mitochondrial tRNA genes
on opposite strands are reported.
-gc Use the GenBank transl_table = genetic code.
-gcstd Use standard genetic code.
-gcmet Use composite Metazoan mitochondrial genetic code.
-gcvert Use Vertebrate mitochondrial genetic code.
-gcinvert Use Invertebrate mitochondrial genetic code.
-gcyeast Use Yeast mitochondrial genetic code.
-gcprot Use Mold/Protozoan/Coelenterate mitochondrial genetic code.
-gcciliate Use Ciliate genetic code.
-gcflatworm Use Echinoderm/Flatworm mitochondrial genetic code
-gceuplot Use Euplotid genetic code.
-gcbact Use Bacterial/Plant Chloroplast genetic code.
-gcaltyeast Use alternative Yeast genetic code.
-gcascid Use Ascidian Mitochondrial genetic code.
-gcaltflat Use alternative Flatworm Mitochondrial genetic code.
-gcblep Use Blepharisma genetic code.
-gcchloroph Use Chlorophycean Mitochondrial genetic code.
-gctrem Use Trematode Mitochondrial genetic code.
-gcscen Use Scenedesmus obliquus Mitochondrial genetic code.
-gcthraust Use Thraustochytrium Mitochondrial genetic code.
Individual modifications can be appended using
,BBB= B = A,C,G, or T. is the three letter
code for an amino-acid. More than one modification
can be specified. eg -gcvert,aga=Trp,agg=Trp uses
the Vertebrate Mitochondrial code and the codons
AGA and AGG changed to Tryptophan.
-tv Do not search for mitochondrial TV replacement
loop tRNA genes. Only relevant if -mt used.
-c7 Search for tRNA genes with 7 base C-loops only.
-i Search for tRNA genes with introns in
anticodon loop with maximum length 3000
bases. Minimum intron length is 0 bases.
Ignored if -m is specified.
-i Search for tRNA genes with introns in
anticodon loop with maximum length
bases. Minimum intron length is 0 bases.
Ignored if -m is specified.
-i, Search for tRNA genes with introns in
anticodon loop with maximum length
bases, and minimum length bases.
Ignored if -m is specified.
-io Same as -i, but allow tRNA genes with long
introns to overlap shorter tRNA genes.
-if Same as -i, but fix intron between positions
37 and 38 on C-loop (one base after anticodon).
-ifo Same as -if and -io combined.
-ir Same as -i, but report tRNA genes with minimum
length bases rather than search for
tRNA genes with minimum length bases.
With this switch, acts as an output filter,
minimum intron length for searching is still 0 bases.
-c Assume that each sequence has a circular
topology. Search wraps around each end.
Default setting.
-l Assume that each sequence has a linear
topology. Search does not wrap.
-d Double. Search both strands of each
sequence. Default setting.
-s or -s+ Single. Do not search the complementary
(antisense) strand of each sequence.
-sc or -s- Single complementary. Do not search the sense
strand of each sequence.
-ps Lower scoring thresholds to 95% of default levels.
-ps Change scoring thresholds to percent of default levels.
-rp Flag possible pseudogenes (score < 100 or tRNA anticodon
loop <> 7 bases long). Note that genes with score < 100
will not be detected or flagged if scoring thresholds are not
also changed to below 100% (see -ps switch).
-seq Print out primary sequence.
-br Show secondary structure of tRNA gene primary sequence
using round brackets.
-fasta Print out primary sequence in fasta format.
-fo Print out primary sequence in fasta format only
(no secondary structure).
-fon Same as -fo, with sequence and gene numbering in header.
-fos Same as -fo, with no spaces in header.
-fons Same as -fo, with sequence and gene numbering, but no spaces.
-w Print out in Batch mode.
-ss Use the stricter canonical 1-2 bp spacer1 and
1 bp spacer2. Ignored if -mt set. Default is to
allow 3 bp spacer1 and 0-2 bp spacer2, which may
degrade selectivity.\n");
-v Verbose. Prints out information during
search to STDERR.
-a Print out tRNA domain for tmRNA genes.
-a7 Restrict tRNA astem length to a maximum of 7 bases
-aa Display message if predicted iso-acceptor species
does not match species in sequence name (if present).
-j Display 4-base sequence on 3' end of astem
regardless of predicted amino-acyl acceptor length.
-jr Allow some divergence of 3' amino-acyl acceptor
sequence from NCCA.
-jr4 Allow some divergence of 3' amino-acyl acceptor
sequence from NCCA, and display 4 bases.
-q Dont print configuration line (which switchs
and files were used).
-rn Repeat sequence name before summary information.
-O Print output to . If
already exists, it is overwritten. By default
all output goes to stdout.
*/
#include
#include
#ifndef SEEK_SET
#define SEEK_SET 0
#define SEEK_CUR 1
#define SEEK_END 2
#endif
#define DLIM '\n'
#define STRLEN 4001
#define STRLENM1 4000
#define SHORTSTRLEN 51
#define SHORTSTRLENM1 50
#define KEYLEN 15
#define INACTIVE 2.0e+35
#define IINACTIVE 2000000001L
#define ITHRESHOLD 2000000000L
#define space(c) (c==' ')||(c=='\t')||(c=='\n')||(c=='\r')
#define sq(pos) ((pos + d->psmax - 1L) % d->psmax) + 1L
#define itmparam(x,y) fputc(x,y)
#define FASTA 0
#define GENBANK 1
#define noGENE -1
#define tRNA 0
#define tmRNA 1
#define srpRNA 2
#define rRNA 3
#define CDS 4
#define NS 6 /* should be one more than number of types of gene */
#define MAXGCMOD 16
#define MAMMAL_MT 2
#define NGENECODE 24
#define METAZOAN_MT 0
#define STANDARD 1
#define VERTEBRATE_MT 2
#define NAMINOACID 27
#define Phe 0
#define Val 1
#define Leu 2
#define Ile 3
#define Cys 4
#define Gly 5
#define Arg 6
#define Ser 7
#define Ala 8
#define Pro 9
#define Thr 10
#define Tyr 11
#define Asp 12
#define His 13
#define Asn 14
#define Met 15
#define Trp 16
#define Glu 17
#define Gln 18
#define Lys 19
#define Stop 20
#define SeC 21
#define Pyl 22
#define INSERT -2
#define TERM -1
#define Adenine 0
#define Cytosine 1
#define Guanine 2
#define Thymine 3
#define AMBIG 4
#define NOBASE 5
#define tRNAthresh 132.0
#define mtRNAdtthresh 91.5
#define mtRNAtthresh 83.5
#define mtRNAdthresh 85.0
#define tmRNAthresh 325.0
#define srpRNAthresh 175.0
#define CDSthresh 100.0
#define PSEUDOGENElevel 0.95
#define RIGHT 0
#define UP 1
#define LEFT 2
#define DOWN 3
#define UPRIGHT 4
#define SLANTDR 5
#define SLANTUR 6
#define SLANTUL 7
#define SLANTDL 8
#define SLANT 5
#define MATX 42 /* 41 */
#define MATY 34
#define ASTEM2_EXT 9
#define ASTEM2_EXTD 4 /* <= ASTEM2_EXT */
#define ASTEM2_EXTE 5 /* ASTEM2_EXT - ASTEM2_EXTD */
#define MINTSTEM_DIST (17 + ASTEM2_EXT)
#define MAXTSTEM_DIST (26 + ASTEM2_EXT)
#define MAXDSTEM_DIST 9
#define MINDSTEM_DIST 8
#define MININTRONLEN 0
#define MAXINTRONLEN 3000
#define MINCTRNALEN 62
#define MAXCTRNALEN 110
#define MINTRNALEN (MINCTRNALEN + 1)
#define MAXTRNALEN (MAXCTRNALEN + ASTEM2_EXT)
#define MAXETRNALEN (MAXTRNALEN + MAXINTRONLEN)
#define VARMAX 26 /* 25 */
#define VARMIN 3
#define VARDIFF 23 /* 22 */ /* VARMAX - VARMIN */
#define MINTPTSDIST 50
#define MAXTPTSDIST 321
#define TPWINDOW (MAXTPTSDIST - MINTPTSDIST + 1)
#define MINTPDIST 50
#define MAXTPDIST 250
#define TPDISTWINDOW (MAXTPDIST - MINTPDIST + 1)
#define MINTAGDIST 12
#define MAXTAGDIST 102
#define TAGWINDOW MAXTAGDIST - MINTAGDIST
#define MINRNACDIST (MINTPDIST - 5)
#define MAXRNACDIST (MAXTPDIST - 5)
#define MAXPPINTRONDIST 250
#define TMPTRAILER 145
#define MINPPASDIST MINTSTEM_DIST
#define MAXPPASDIST MAXTSTEM_DIST + MAXPPINTRONDIST
#define MINPPTSTPDIST MINTSTEM_DIST + MINTPDIST
#define MAXPPTSTPDIST MAXTSTEM_DIST+ASTEM2_EXT+MAXTPDIST+MAXPPINTRONDIST
#define MAXTMRNALEN (4 + MAXPPASDIST + MAXTPDIST + MAXTAGDIST + TMPTRAILER)
#define TSWEEP 1000
#define WRAP 2*MAXETRNALEN
#define NPTAG 33
/*
NOTE: If MAXPPINTRONDIST is increased, then validity of MAXTMRNALEN
and MAXETRNALEN must be ensured. WRAP = 2*MAXETRNALEN determines the length
of wseq, which contains the wrap around for circular sequences. This
must remain equal to or more than 2*MAXTMRNALEN and TSWEEP.
*/
#define BASE 0
#define FSTEM 1
#define BSTEM 2
#define NOID 0
#define DLOOP 1
#define DSTEM 2
#define CLOOP 3
#define VAR 4
#define NA MAXINTRONLEN
#define ND 100
#define NT 200
#define NH 2000
#define NTH 3000
#define NC 5000
#define NGFT 5000 /* 100 */
#define NTAG 474 /* 367 */
#define LSEQ 20000
#define ATBOND 2.5
#define mtNA 1500
#define mtND 150
#define mtNTH 3000 /* 750 */
#define mtNTM 3
#define mtNCDS 200 /* 500,20 */
#define mtNCDSCODON 6000
#define mtGCBOND 0.0
#define mtATBOND -0.5
#define mtGTBOND -1.2
#define mtTTBOND -2.9
#define mtGGBOND -3.0
#define mtGABOND -3.0
#define mtNOBOND -3.0
#define mtBONDSTAB 1.5
#define mtABONDSTAB 2.0
#define mtTSTTSTAB -2.5
#define mtTERMSTAB 0.01
#define mtSENDSTAB 0.01
#define mtNSTAB 0.1
#define mt3MMSTAB 1.0
#define mtGCPENALTY 0.8
#define mtGCPENALTYD 2.0
#define mt_DRLmaxlength 16
#define mt_TVRLmaxlength 18
#define mtNCLM 3
#define SRRNAMAXLEN 1500
#define SRRNAMINLEN 600
#define LRRNAMINLEN 1200
#define LRRNAMAXLEN 3000
#define srpMAXLEN 650
#define srpUMAXLEN 300
#define srpUMINLEN 100
#define srpDMAXLEN 300
#define srpDMINLEN 100
#define srpNH 200
#define srpNS 500 /* 100 */
#define srpMAXHPL 14
#define srpMAXSP 6
#define srpMAXSTEM 6500 /* 6000 */
#define srpDISPMAX 4*srpMAXLEN
#define srpMAXSPACER 12
#define srpMAXNISTEMS 10
#define srpNESTMAX 2 /* 3 */
#define cdsMAXLEN 3000
#define NCDS 200
#define NCDSCODON 1000
typedef struct { long start;
long stop;
int comp;
long antistart;
long antistop;
int genetype;
char species[SHORTSTRLEN]; } annotated_gene;
typedef struct { char filename[80];
FILE *f;
char seqname[STRLEN];
int datatype;
double gc;
long ps;
long psmax;
long seqstart;
long nextseq;
int ns;
int nagene[NS];
annotated_gene gene[NGFT]; } data_set;
typedef struct { char name[80];
int seq[MAXTRNALEN+1];
int eseq[MAXETRNALEN+1];
int *ps;
int nbase;
int comp;
long start;
long stop;
int astem1;
int astem2;
int aatail;
int spacer1;
int spacer2;
int dstem;
int dloop;
int cstem;
int cloop;
int intron;
int nintron;
int anticodon;
int var;
int varbp;
int tstem;
int tloop;
int genetype;
double energy;
int asst;
int tps;
int tpe; } gene;
typedef struct { int *pos;
int stem;
int loop;
double energy; } trna_loop;
typedef struct { int *pos;
int stem;
int loop;
unsigned int bondtype;
double energy;
double stem_energy; } mt_trna_loop;
typedef struct { int *pos;
int *looppos;
int *end;
int stem;
int loop;
int arm;
int anticodon;
unsigned int bondtype;
double energy;
double stem_energy; } mt_trna_cloop;
typedef struct { int *pos;
int stem;
int loop;
int *end;
unsigned int bondtype;
double energy;
double stem_energy; } mt_trna_tloop;
typedef struct { int *pos;
int *end;
int stem;
int loop;
double energy; } trna_dloop;
typedef struct { int *pos1;
int *pos2;
int stem;
double energy; } trna_astem;
typedef struct { int *pos1;
int *pos2;
int stem;
unsigned int bondtype;
double energy; } mt_trna_astem;
typedef struct { int *pos;
int comp;
int frame;
int codon;
int win; } mt_cds_codon;
typedef struct { int *pos1;
int *pos2;
int comp; } mt_cds;
typedef struct { int *pos1;
int *pos2;
int comp; } mt_rrna;
typedef struct { int *pos1;
int *pos2;
int stem;
int loop; } rrna_hairpin;
typedef struct { int *pos1;
int *pos2;
int stem; } rrna_stem;
typedef struct { int *pos;
int comp;
int frame;
int codon;
int win; } cds_codon;
typedef struct { FILE *f;
int batch;
int repeatsn;
int trna;
int tmrna;
int srprna;
int cds;
int mtrna;
int tvloop;
int cloop7;
int peptide;
int geneticcode;
int ngcmod;
int gcmod[MAXGCMOD];
int gcfix;
int discrim;
int extastem;
int tarm;
int tagthresh;
int tarmlength;
int showconfig;
int libflag;
int verbose;
int linear;
int both;
int reportpseudogenes;
int energydisp;
int secstructdisp;
int seqdisp;
int aataildisp;
int aataildiv;
int sp1max;
int sp2min;
int sp2max;
int mtxdetect;
int mtcdsscan;
int mtcompov;
int matchacceptor;
int maxintronlen;
int minintronlen;
int minintronlenreport;
int ioverlay;
int ifixedpos;
int ireportminintronlen;
int tmstrict;
int iamismatch;
int loffset;
int roffset;
long start;
int comp;
int genespace;
int srpspace;
int ngene[NS];
int nps;
int annotated;
int nagene[NS];
int natfn;
int natfp;
int natfpd;
int natfptv;
int nacdsfn;
int nacdsfp;
int lacds;
int ldcds;
long nabase;
double trnathresh;
double ttscanthresh;
double ttarmthresh;
double tdarmthresh;
double tastemthresh;
double tascanthresh;
double mttthresh;
double mtdthresh;
double mtdtthresh;
double mttarmthresh;
double mtdarmthresh;
double tmrnathresh;
double tmathresh;
double tmcthresh;
double tmcathresh;
double tmrthresh;
double srpthresh;
double cdsthresh;
double eref[NS];
int tmrna_struct[200];
} csw;
/* Basepair matching matrices */
int lbp[3][6][6] =
{ { { 0,0,1,1,1,0 },
{ 0,0,1,0,1,0 },
{ 1,1,0,1,1,0 },
{ 1,0,1,0,1,0 },
{ 1,1,1,1,1,0 },
{ 0,0,0,0,0,0 } },
{ { 0,0,0,1,1,0 },
{ 0,0,1,0,1,0 },
{ 0,1,0,1,1,0 },
{ 1,0,1,0,1,0 },
{ 1,1,1,1,1,0 },
{ 0,0,0,0,0,0 } },
{ { 0,0,0,1,1,0 },
{ 0,0,1,0,1,0 },
{ 0,1,0,0,1,0 },
{ 1,0,0,0,1,0 },
{ 1,1,1,1,1,0 },
{ 0,0,0,0,0,0 } } };
int bp[6][6] = { { 0,0,0,1,1,0 },
{ 0,0,1,0,1,0 },
{ 0,1,0,1,1,0 },
{ 1,0,1,0,1,0 },
{ 1,1,1,1,1,0 },
{ 0,0,0,0,0,0 } };
int wbp[6][6] =
{ { 0,0,0,2,2,0 },
{ 0,0,2,0,2,0 },
{ 0,2,0,1,2,0 },
{ 2,0,1,0,2,0 },
{ 2,2,2,2,2,0 },
{ 0,0,0,0,0,0 } };
int wcbp[6][6] = { { 0,0,0,1,1,0 },
{ 0,0,1,0,1,0 },
{ 0,1,0,0,1,0 },
{ 1,0,0,0,1,0 },
{ 1,1,1,1,1,0 },
{ 0,0,0,0,0,0 } };
int gc[6][6] = { { 0,0,0,0,0,0 },
{ 0,0,1,0,1,0 },
{ 0,1,0,0,1,0 },
{ 0,0,0,0,0,0 },
{ 0,1,1,0,1,0 },
{ 0,0,0,0,0,0 } };
int gt[6][6] = { { 0,0,0,0,0,0 },
{ 0,0,0,0,0,0 },
{ 0,0,0,1,1,0 },
{ 0,0,1,0,1,0 },
{ 0,0,1,1,1,0 },
{ 0,0,0,0,0,0 } };
int at[6][6] = { { 0,0,0,1,1,0 },
{ 0,0,0,0,0,0 },
{ 0,0,0,0,0,0 },
{ 1,0,0,0,0,0 },
{ 1,0,0,0,1,0 },
{ 0,0,0,0,0,0 } };
int tt[6][6] = { { 0,0,0,0,0,0 },
{ 0,0,0,0,0,0 },
{ 0,0,0,0,0,0 },
{ 0,0,0,1,1,0 },
{ 0,0,0,1,1,0 },
{ 0,0,0,0,0,0 } };
int stemterm[6][6] = { { 0,0,1,0,1,0 },
{ 0,0,0,0,0,0 },
{ 1,0,0,0,1,0 },
{ 0,0,0,1,1,0 },
{ 1,0,1,1,1,0 },
{ 0,0,0,0,0,0 } };
int aastemterm[6][6] =
{ { 1,0,1,0,1,0 },
{ 0,0,0,0,0,0 },
{ 1,0,0,0,1,0 },
{ 0,0,0,1,1,0 },
{ 1,0,1,1,1,0 },
{ 0,0,0,0,0,0 } };
int ggstemterm[6][6] =
{ { 0,0,1,0,1,0 },
{ 0,0,0,0,0,0 },
{ 1,0,1,0,1,0 },
{ 0,0,0,1,1,0 },
{ 1,0,1,1,1,0 },
{ 0,0,0,0,0,0 } };
int assymst[6][6] = { { 0,0,0,0,0,0 },
{ 0,0,0,0,0,0 },
{ 1,0,0,0,1,0 },
{ 0,0,0,1,1,0 },
{ 1,0,0,1,1,0 },
{ 0,0,0,0,0,0 } };
int assymat[6][6] = { { 0,0,0,1,1,0 },
{ 0,0,0,0,0,0 },
{ 0,0,0,0,0,0 },
{ 0,0,0,0,0,0 },
{ 0,0,0,1,1,0 },
{ 0,0,0,0,0,0 } };
int stackbp[6][6] = { { 0,0,0,1,1,0 },
{ 0,0,1,0,1,0 },
{ 0,1,0,1,1,0 },
{ 1,0,1,1,1,0 },
{ 1,1,1,1,1,0 },
{ 0,0,0,0,0,0 } };
int ggstackbp[6][6] =
{ { 0,0,0,1,1,0 },
{ 0,0,1,0,1,0 },
{ 0,1,1,1,1,0 },
{ 1,0,1,1,1,0 },
{ 1,1,1,1,1,0 },
{ 0,0,0,0,0,0 } };
int ggbp[6][6] =
{ { 0,0,0,1,1,0 },
{ 0,0,1,0,1,0 },
{ 0,1,1,1,1,0 },
{ 1,0,1,0,1,0 },
{ 1,1,1,1,1,0 },
{ 0,0,0,0,0,0 } };
int gabp[6][6] =
{ { 0,0,1,1,1,0 },
{ 0,0,1,0,1,0 },
{ 1,1,0,1,1,0 },
{ 1,0,1,0,1,0 },
{ 1,1,1,1,1,0 },
{ 0,0,0,0,0,0 } };
int assymagbp[6][6] =
{ { 0,0,1,1,1,0 },
{ 0,0,1,0,1,0 },
{ 0,1,0,1,1,0 },
{ 1,0,1,0,1,0 },
{ 1,1,1,1,1,0 },
{ 0,0,0,0,0,0 } };
int stembp[6][6] =
{ { 0,0,1,1,1,0 },
{ 0,0,1,0,1,0 },
{ 1,1,0,1,1,0 },
{ 1,0,1,1,1,0 },
{ 1,1,1,1,1,0 },
{ 0,0,0,0,0,0 } };
int ggstembp[6][6] =
{ { 0,0,1,1,1,0 },
{ 0,0,1,0,1,0 },
{ 1,1,1,1,1,0 },
{ 1,0,1,1,1,0 },
{ 1,1,1,1,1,0 },
{ 0,0,0,0,0,0 } };
int gastembp[6][6] =
{ { 1,0,1,1,1,0 },
{ 0,0,1,0,1,0 },
{ 1,1,1,1,1,0 },
{ 1,0,1,1,1,0 },
{ 1,1,1,1,1,0 },
{ 0,0,0,0,0,0 } };
int vbp[6][6] =
{ { 0,0,1,4,4,0 },
{ 0,0,4,0,4,0 },
{ 1,4,0,2,4,0 },
{ 4,0,2,0,4,0 },
{ 4,4,4,4,4,0 },
{ 0,0,0,0,0,0 } };
int tandemid[mtNTM][4] =
{ { 3,2,2,3 },
{ 2,3,3,2 },
{ 3,3,3,3 } };
double tandem_em[mtNTM] = { -0.5,-0.5,2.0 };
double send_em[6][6] =
{ { 0.0,0.0,0.0,0.0,0.0,0.0 },
{ 0.0,0.0,0.5*mtSENDSTAB,0.0,0.5*mtSENDSTAB,0.0 },
{ 0.0,0.5*mtSENDSTAB,0.0,mtSENDSTAB,mtSENDSTAB,0.0 },
{ 0.0,0.0,mtSENDSTAB,0.0,mtSENDSTAB,0.0 },
{ 0.0,0.5*mtSENDSTAB,mtSENDSTAB,mtSENDSTAB,mtSENDSTAB,0.0 },
{ 0.0,0.0,0.0,0.0,0.0,0.0 } };
double ssend_em[6][6] =
{ { 0.0,0.0,0.0,0.0,0.0,0.0 },
{ 0.0,0.0,mtSENDSTAB,0.0,mtSENDSTAB,0.0 },
{ 0.0,mtSENDSTAB,0.0,mtSENDSTAB,mtSENDSTAB,0.0 },
{ 0.0,0.0,mtSENDSTAB,0.0,mtSENDSTAB,0.0 },
{ 0.0,mtSENDSTAB,mtSENDSTAB,mtSENDSTAB,mtSENDSTAB,0.0 },
{ 0.0,0.0,0.0,0.0,0.0,0.0 } };
int neighbour_map[6][6] =
{ { 0,0,1,0,1,0 },
{ 0,0,0,0,0,0 },
{ 1,0,0,0,1,0 },
{ 0,0,0,1,1,0 },
{ 1,0,1,1,1,0 },
{ 0,0,0,0,0,0 } };
double neighbour_em[2][6][6] = {
{ { 0.0,0.0,0.0,0.0,0.0,0.0 },
{ 0.0,0.0,0.0,0.0,0.0,0.0 },
{ 0.0,0.0,0.0,0.0,0.0,0.0 },
{ 0.0,0.0,0.0,0.0,0.0,0.0 },
{ 0.0,0.0,0.0,0.0,0.0,0.0 },
{ 0.0,0.0,0.0,0.0,0.0,0.0 } },
{ { 0.0,0.0,0.0,0.0,0.0,0.0 },
{ 0.0,0.0,mtNSTAB,0.0,mtNSTAB,0.0 },
{ 0.0,mtNSTAB,0.0,0.0,mtNSTAB,0.0 },
{ 0.0,0.0,0.0,0.0,0.0,0.0 },
{ 0.0,mtNSTAB,mtNSTAB,0.0,mtNSTAB,0.0 },
{ 0.0,0.0,0.0,0.0,0.0,0.0 } } };
unsigned int btmap[6][6] =
{ { 0x10000,0x10000,0x1000,0x10,0x00000,0x10000 },
{ 0x10000,0x10000,0x1,0x10000,0x00000,0x10000 },
{ 0x1000,0x1,0x10000,0x100,0x00000,0x10000 },
{ 0x10,0x10000,0x100,0x1000,0x00000,0x10000 },
{ 0x00000,0x00000,0x00000,0x00000,0x00000,0x10000 },
{ 0x10000,0x10000,0x10000,0x10000,0x10000,0x10000 } };
double bem[6][6] =
{ { -2.144,-0.428,-2.144, ATBOND, 0.000, 0.000 },
{ -0.428,-2.144, 3.000,-2.144, 0.000, 0.000 },
{ -2.144, 3.000,-2.144, 1.286, 0.000, 0.000 },
{ ATBOND,-2.144, 1.286,-0.428, 0.000, 0.000 },
{ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000 },
{ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000 } };
int mt_discrim[3][64][6] =
/* metazoan mt */
{{{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 0,0,0,0,0,0 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 0,0,0,0,0,0 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }},
/* standard */
{{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }, { 1,1,1,1,1,1 }},
/* mammal mt */
{{ 1,0,0,0,1,1 }, { 1,0,0,0,1,1 }, { 1,0,0,0,1,1 }, { 1,0,0,0,1,1 },
{ 0,0,0,1,1,1 }, { 1,0,0,0,1,1 }, { 1,0,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,0,1,0,1,1 }, { 1,0,0,0,1,1 }, { 1,1,1,1,1,1 },
{ 1,0,0,0,1,1 }, { 1,1,1,1,1,1 }, { 0,1,0,0,1,1 }, { 0,0,1,0,1,1 },
{ 1,0,0,0,1,1 }, { 1,0,0,0,1,1 }, { 1,0,0,0,1,1 }, { 1,0,1,0,1,1 },
{ 0,0,1,0,1,1 }, { 1,0,0,0,1,1 }, { 1,0,1,1,1,1 }, { 1,0,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,0,1,0,1,1 }, { 1,0,0,0,1,1 }, { 1,1,1,1,1,1 },
{ 0,0,0,0,0,0 }, { 1,0,1,1,1,1 }, { 0,0,1,0,1,1 }, { 1,1,1,1,1,1 },
{ 1,0,0,0,1,1 }, { 1,0,0,0,1,1 }, { 1,0,0,0,1,1 }, { 1,0,1,0,1,1 },
{ 0,1,0,1,1,1 }, { 1,0,0,0,1,1 }, { 1,0,1,1,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,1,1,1,1 }, { 1,0,1,0,1,1 }, { 1,0,0,0,1,1 }, { 1,1,1,1,1,1 },
{ 1,1,0,0,1,1 }, { 1,1,1,1,1,1 }, { 0,1,0,0,1,1 }, { 0,0,1,0,1,1 },
{ 1,1,0,1,1,1 }, { 1,0,0,0,1,1 }, { 1,0,1,1,1,1 }, { 1,0,0,0,1,1 },
{ 1,0,1,0,1,1 }, { 1,0,0,0,1,1 }, { 1,1,1,1,1,1 }, { 0,0,0,0,0,0 },
{ 1,1,1,1,1,1 }, { 1,0,1,0,1,1 }, { 1,0,1,0,1,1 }, { 1,1,1,1,1,1 },
{ 1,0,0,0,1,1 }, { 1,1,1,1,1,1 }, { 1,0,1,0,1,1 }, { 1,1,1,1,1,1 }}};
/* GENETIC CODES (INDEXED BY ANTICODON) */
char aapolarity[NAMINOACID+1] = "NNNNPNPPNNPNPPPNNPPP***????";
char aaletter[NAMINOACID+1] = "FVLICGRSAPTYDHNMWEQK***????";
char aaname[NAMINOACID][20] =
{ "Phe","Val","Leu","Ile","Cys",
"Gly","Arg","Ser","Ala","Pro",
"Thr","Tyr","Asp","His","Asn",
"Met","Trp","Glu","Gln","Lys",
"Stop",
"seC",
"Pyl",
"(Arg|Stop|Ser|Gly)",
"(Ile|Met)",
"(Stop|Trp)",
"(Lys|Asn)" };
char ambig_aaname[4] = "???";
int aamap[NGENECODE][64] = {
/* composite metazoan mt */
{ Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Met,
Trp,Gly,Arg,23,
Ser,Ala,Pro,Thr,
Pyl,Glu,Gln,Lys,
Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,24,
25,Gly,Arg,23,
Ser,Ala,Pro,Thr,
Stop,Glu,Gln,26 },
/* standard */
{ Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Met,
Trp,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Pyl,Glu,Gln,Lys,
Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Ile,
SeC,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Stop,Glu,Gln,Lys },
/* vertebrate mt */
{ Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Met,
Trp,Gly,Arg,Stop,
Ser,Ala,Pro,Thr,
Pyl,Glu,Gln,Lys,
Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Met,
Trp,Gly,Arg,Stop,
Ser,Ala,Pro,Thr,
Stop,Glu,Gln,Lys },
/* yeast mt */
{ Phe,Val,Thr,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Thr,Met,
Trp,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Pyl,Glu,Gln,Lys,
Phe,Val,Thr,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Thr,Met,
Trp,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Stop,Glu,Gln,Lys },
/* mold, protozoan, and coelenterate mt */
{ Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Met,
Trp,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Pyl,Glu,Gln,Lys,
Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Ile,
Trp,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Stop,Glu,Gln,Lys },
/* invertebrate mt */
{ Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Met,
Trp,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Pyl,Glu,Gln,Lys,
Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Met,
Trp,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Stop,Glu,Gln,Lys },
/* ciliate */
{ Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Met,
Trp,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Gln,Glu,Gln,Lys,
Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Ile,
SeC,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Gln,Glu,Gln,Lys },
/* deleted -> standard */
{ Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Met,
Trp,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Pyl,Glu,Gln,Lys,
Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Ile,
SeC,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Stop,Glu,Gln,Lys },
/* deleted -> standard */
{ Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Met,
Trp,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Pyl,Glu,Gln,Lys,
Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Ile,
SeC,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Stop,Glu,Gln,Lys },
/* echinoderm and flatworm mt */
{ Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Met,
Trp,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Pyl,Glu,Gln,Lys,
Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Ile,
Trp,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Stop,Glu,Gln,Asn },
/* euplotid */
{ Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Met,
Trp,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Pyl,Glu,Gln,Lys,
Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Ile,
Cys,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Stop,Glu,Gln,Lys },
/* bacterial and plant chloroplast */
{ Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Ser,Met,
Trp,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Pyl,Glu,Gln,Lys,
Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Ile,
SeC,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Stop,Glu,Gln,Lys },
/* alternate yeast */
{ Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Ser,Met,
Trp,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Pyl,Glu,Gln,Lys,
Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Ile,
SeC,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Stop,Glu,Gln,Lys },
/* ascidian mt */
{ Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Met,
Trp,Gly,Arg,Gly,
Ser,Ala,Pro,Thr,
Pyl,Glu,Gln,Lys,
Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Met,
Trp,Gly,Arg,Gly,
Ser,Ala,Pro,Thr,
Stop,Glu,Gln,Lys },
/* alternate flatworm mt */
{ Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Met,
Trp,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Pyl,Glu,Gln,Lys,
Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Ile,
Trp,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Glu,Gln,Asn },
/* blepharisma */
{ Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Met,
Trp,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Gln,Glu,Gln,Lys,
Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Ile,
SeC,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Stop,Glu,Gln,Lys },
/* chlorophycean mt */
{ Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Met,
Trp,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Leu,Glu,Gln,Lys,
Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Ile,
SeC,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Stop,Glu,Gln,Lys },
/* deleted -> standard */
{ Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Met,
Trp,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Pyl,Glu,Gln,Lys,
Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Ile,
SeC,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Stop,Glu,Gln,Lys },
/* deleted -> standard */
{ Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Met,
Trp,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Pyl,Glu,Gln,Lys,
Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Ile,
SeC,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Stop,Glu,Gln,Lys },
/* deleted -> standard */
{ Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Met,
Trp,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Pyl,Glu,Gln,Lys,
Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Ile,
SeC,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Stop,Glu,Gln,Lys },
/* deleted -> standard */
{ Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Met,
Trp,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Pyl,Glu,Gln,Lys,
Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Ile,
SeC,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Stop,Glu,Gln,Lys },
/* trematode mt */
{ Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Met,
Trp,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Pyl,Glu,Gln,Lys,
Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Met,
Trp,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Stop,Glu,Gln,Lys },
/* scenedesmus obliquus mt*/
{ Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Met,
Trp,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Leu,Glu,Gln,Lys,
Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Leu,Ile,
SeC,Gly,Arg,Arg,
Stop,Ala,Pro,Thr,
Stop,Glu,Gln,Lys },
/* thraustochytrium mt */
{ Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Leu,Val,Ser,Met,
Trp,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Pyl,Glu,Gln,Lys,
Phe,Val,Leu,Ile,
Cys,Gly,Arg,Ser,
Ser,Ala,Pro,Thr,
Tyr,Asp,His,Asn,
Stop,Val,Leu,Ile,
SeC,Gly,Arg,Arg,
Ser,Ala,Pro,Thr,
Stop,Glu,Gln,Lys } };
/* POINTERS TO DETECTED GENES */
gene *ts;
/* TOOLS */
char upcasec(char c)
{ return((c >= 'a')?c-32:c); }
int length(char *s)
{ int i=0;
while (*s++) i++;
return(i); }
char *strpos(char *s, char *k)
{ char c,d;
int i;
d = *k;
while (c = *s)
{ if (c == d)
{ i = 0;
do if (!k[++i]) return(s); while (s[i] == k[i]); }
s++; }
return(NULL); }
char *softstrpos(char *s, char *k)
{ char c,d;
int i;
d = upcasec(*k);
while (c = *s)
{ if (upcasec(c) == d)
{ i = 0;
do if (!k[++i]) return(s);
while (upcasec(s[i]) == upcasec(k[i])); }
s++; }
return(NULL); }
char *marginstring(char *s, char *k, int margin)
{ char c,d;
int i,j;
j = 0;
d = *k;
while (c = *s)
{ if (c == d)
{ i = 0;
do if (!k[++i]) return(s); while (s[i] == k[i]); }
s++;
if (++j >= margin) break; }
return(NULL); }
int margindetect(char *line, int margin)
{ int i;
char c,*s;
i = 0;
s = line;
while (c = *s++)
{ if (!space(c)) break;
if (c == '\t') i += 7;
if (++i >= margin) return(0); }
if (c == '\n') return(0);
if (c == '\r') return(0);
if (c == '\0') return(0);
return(1); }
char *dconvert(char *s, double *r)
{ static char zero='0',nine='9';
int shift,expshift,sgn,expsgn,exponent;
char c,limit;
double result;
shift = 0;
expshift = 0;
sgn = 1;
expsgn = 1;
limit = 0;
exponent = 0;
result = 0.0;
if ((c = *s) == '-')
{ sgn = -1;
c = *++s; }
else if (c == '+') c= *++s;
if (c >= zero)
if (c <= nine)
{ result = (double)(c - zero);
while ((c = *++s) >= zero)
{ if (c > nine) break;
if (++limit < 15) result = result*10.0 + (double)(c - zero); }}
if (c == '.')
while ((c = *++s) >= zero)
{ if (c > nine) break;
if (++limit < 15)
{ result = result*10.0 + (double)(c - zero);
shift++; }}
if ((c == 'E')||(c == 'e')||(c == 'D')||(c == 'd'))
{ if ((c = *++s) == '-')
{ expsgn = -1;
c = *++s; }
else
if (c == '+') c = *++s;
if (c >= zero)
if (c <= nine)
{ exponent = c - zero;
while ((c = *++s) >= zero)
{ if (c > nine) break;
exponent = exponent*10 + c - zero;
if (++expshift > 3) break; }}}
result *= (double)sgn;
exponent = exponent*expsgn - shift;
if (exponent >= 0)
while (exponent--) result *= 10.0;
else
while (exponent++) result /= 10.0;
(*r) *= 0.01*result;
return(s); }
char *lconvert(char *s, long *r)
{ static char zero='0',nine='9';
long sgn;
long result;
char c;
sgn = 1L;
result = 0L;
if ((c = *s) == '-')
{ sgn = -1L;
c = *++s; }
else if (c == '+') c= *++s;
if (c >= zero)
if (c <= nine)
{ result = (long)(c - zero);
while ((c = *++s) >= zero)
{ if (c > nine) break;
result = result*10L + (long)(c - zero); }}
*r = result * sgn;
return(s); }
char *getlong(char *line, long *l)
{ static char zero='0',nine='9';
char c1,c2,*s;
s = line;
while (c1 = *s)
{ if (c1 >= zero)
{ if (c1 <= nine) return(lconvert(s,l)); }
else
if ((c1 == '-') || (c1 == '+'))
{ c2 = s[1];
if (c2 >= zero)
if (c2 <= nine)
return(lconvert(s,l)); }
s++; }
return(NULL); }
char *copy(char *from, char *to)
{ while (*to++ = *from++);
return(--to); }
char *copy3cr(char *from, char *to, int n)
{ while (*to = *from++)
{ if (*to == DLIM)
{ *to = '\0';
break; }
if (--n <= 0)
{ *++to = '\0';
break; }
to++; }
return(to); }
char *quotestring(char *line, char *a, int n)
{ char ch;
while (ch = *line++)
if (ch == '"')
{ while (ch = *line++)
if (ch != '"')
{ *a++ = ch;
if (--n <= 0) break; }
else break;
break; }
*a = '\0';
return(a); }
/* LIBRARY */
long process_sequence_heading(data_set *d, csw *sw)
{ int i,ic,nagene;
long l,realstart;
char line[STRLEN],c,*s,*sq;
annotated_gene *agene;
FILE *f;
f = d->f;
d->datatype = FASTA;
fseek(f,d->seqstart,SEEK_SET);
do { if ((ic = getc(f)) == EOF) return(-1L);
c = (char)ic; }
while (space(c));
if (!fgets(d->seqname,STRLENM1,f)) return(-1L);
if (c != '>')
{ if (upcasec(c) != 'L') goto FNSN;
if (!(s = softstrpos(d->seqname,"OCUS"))) goto FNSN;
s += 4;
while (space(*s)) s++;
sq = d->seqname;
while (!space(*s)) *sq++ = *s++;
*sq++ = ' ';
if (!fgets(line,STRLENM1,f)) return(-1L);
if (!(s = softstrpos(line,"DEFINITION"))) return(-1L);
s += 10;
while (space(*s)) s++;
copy(s,sq);
if (!fgets(line,STRLENM1,f)) return(-1L);
for (i = 0; i < NS; i++) d->nagene[i] = 0;
nagene = 0;
while (!marginstring(line,"ORIGIN",10))
{ if (nagene >= NGFT) goto GBNL;
if (!(s = marginstring(line,"tRNA",10))) goto CDSEQ;
agene = &(d->gene[nagene]);
agene->genetype = tRNA;
if (softstrpos(s,"complement")) agene->comp = 1;
else agene->comp = 0;
if (!(s = getlong(s,&l))) l = -1L;
agene->start = l;
if (!(s = getlong(s,&l))) l = -1L;
agene->stop = l;
copy("tRNA-???",agene->species);
agene->antistart = -1L;
agene->antistop = -1L;
if (!fgets(line,STRLENM1,f)) return(-1L);
while (!margindetect(line,10))
{ if (s = softstrpos(line,"product="))
if (s = softstrpos(s,"tRNA-"))
{ s += 5;
while (space(*s)) s++;
copy3cr(s,agene->species+5,3); }
if (s = softstrpos(line,"anticodon="))
{ s += 10;
if (!(s = getlong(s,&l))) l = -1L;
agene->antistart = l;
if (!(s = getlong(s,&l))) l = -1L;
agene->antistop = l; }
if (!fgets(line,STRLENM1,f)) return(-1L); }
d->nagene[tRNA]++;
nagene++;
continue;
CDSEQ:
if (!(s = marginstring(line,"CDS",10)))
if (!(s = marginstring(line,"mRNA",10)))
goto RRNA;
agene = &(d->gene[nagene]);
agene->genetype = CDS;
if (softstrpos(s,"complement")) agene->comp = 1;
else agene->comp = 0;
if (!(s = getlong(s,&l))) l = -1L;
agene->start = l;
if (!(s = getlong(s,&l))) l = -1L;
agene->stop = l;
copy("???",agene->species);
if (!fgets(line,STRLENM1,f)) return(-1L);
while (!margindetect(line,10))
{ if (s = softstrpos(line,"gene="))
{ s += 5;
quotestring(s,agene->species,SHORTSTRLENM1); }
else if (s = softstrpos(line,"product="))
{ s += 8;
quotestring(s,agene->species,SHORTSTRLENM1); }
if (!fgets(line,STRLENM1,f)) return(-1L); }
d->nagene[CDS]++;
nagene++;
continue;
RRNA:
if (!(s = marginstring(line,"rRNA",10))) goto GBNL;
agene = &(d->gene[nagene]);
agene->genetype = rRNA;
if (softstrpos(s,"complement")) agene->comp = 1;
else agene->comp = 0;
if (!(s = getlong(s,&l))) l = -1L;
agene->start = l;
if (!(s = getlong(s,&l))) l = -1L;
agene->stop = l;
copy("???",agene->species);
if (!fgets(line,STRLENM1,f)) return(-1L);
while (!margindetect(line,10))
{ if (s = softstrpos(line,"gene="))
{ s += 5;
quotestring(s,agene->species,SHORTSTRLENM1); }
else if (s = softstrpos(line,"product="))
{ s += 8;
quotestring(s,agene->species,SHORTSTRLENM1); }
if (!fgets(line,STRLENM1,f)) return(-1L); }
d->nagene[rRNA]++;
nagene++;
continue;
GBNL:
if (!fgets(line,STRLENM1,f)) return(-1L); }
d->datatype = GENBANK;
d->nagene[NS-1] = nagene;
sw->annotated = 1;
realstart = ftell(f); }
else
{ MH:
realstart = ftell(f);
do { if ((ic = getc(f)) == EOF) return(-1L);
c = (char)ic; }
while (space(c));
if (c == '>')
{ if (!fgets(line,STRLENM1,f)) return(-1L);
goto MH; }
fseek(f,realstart,SEEK_SET); }
s = d->seqname;
i = 0;
while ((c = *s) != '\0')
{ if (c == '\n') break;
if (c == '\r') break;
if (++i >= STRLEN) break;
s++; }
*s = '\0';
return(realstart);
FNSN:
realstart = d->seqstart;
s = copy("Unnamed sequence ",d->seqname);
fseek(f,realstart,SEEK_SET);
if (fgets(line,STRLENM1,f)) copy3cr(line,s,50);
fseek(f,realstart,SEEK_SET);
return(realstart); }
int move_forward(data_set *d)
{ int ic;
long nextbase;
static int map[256] =
{ -4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,
-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,
-4,-4,-4,-4,-4,-4,NOBASE,-3,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,
-4,-4,-2,-4,-4,Adenine,AMBIG,Cytosine,AMBIG,-4,-4,Guanine,AMBIG,
-4,-4,AMBIG,-5,AMBIG,AMBIG,-4,-4,-4,
AMBIG,AMBIG,Thymine,Thymine,AMBIG,AMBIG,-4,
AMBIG,-4,-4,-4,-4,INSERT,NOBASE,-4,Adenine,AMBIG,Cytosine,AMBIG,
-4,-4,Guanine,AMBIG,-4,-4,AMBIG,-5,AMBIG,AMBIG,-4,-4,-4,
AMBIG,AMBIG,Thymine,Thymine,AMBIG,AMBIG,-4,
AMBIG,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,
-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,
-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,
-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,
-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,
-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,
-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4,-4 };
if (d->ps >= d->psmax)
if (d->psmax > 0L)
{ fseek(d->f,d->seqstart,SEEK_SET);
d->ps = 0L; }
NL:
if ((ic = getc(d->f)) == EOF) goto FAIL;
SC:
ic = map[ic];
BS:
if (ic >= Adenine)
{ d->ps++;
return(ic); }
if (ic == -2)
{ d->nextseq = ftell(d->f) - 1L;
return(TERM); }
if (ic == -3)
if (d->datatype == GENBANK)
{ if ((ic = getc(d->f)) == EOF) goto FAIL;
if ((ic = map[ic]) != -3) goto BS;
do if ((ic = getc(d->f)) == EOF) goto FAIL;
while (space(ic));
d->nextseq = ftell(d->f) - 1L;
return(TERM); }
if (ic == -5)
{ nextbase = ftell(d->f);
if ((ic = getc(d->f)) == EOF) goto FAIL;
if (upcasec(ic) == 'O')
{ if ((ic = getc(d->f)) == EOF) goto FAIL;
if (upcasec(ic) == 'C')
{ if ((ic = getc(d->f)) == EOF) goto FAIL;
if (upcasec(ic) == 'U')
{ if ((ic = getc(d->f)) == EOF) goto FAIL;
if (upcasec(ic) == 'S')
{ d->nextseq = nextbase - 1L;
return(TERM); }}}}
fseek(d->f,nextbase,SEEK_SET); }
goto NL;
FAIL:
d->nextseq = -1L;
if (d->psmax > 0L)
{ d->ps = d->psmax;
return(NOBASE); }
else return(TERM); }
int seq_init(data_set *d, csw *sw)
{ long ngc;
int ic;
if ((d->seqstart = process_sequence_heading(d,sw)) < 0L) return(0);
d->ps = 0L;
d->psmax = -1L;
ngc = 0L;
while ((ic = move_forward(d)) >= Adenine)
if (ic >= Cytosine)
if (ic <= Guanine)
ngc++;
if ((d->psmax = d->ps) <= 0L) return(0);
d->gc = (double)ngc/(double)d->psmax;
fseek(d->f,d->seqstart,SEEK_SET);
d->ps = 0L;
return(1); }
char cbase(int c)
{ static char base[6] = "acgt..";
if (c < Adenine) return('#');
if (c > NOBASE) return((char)c);
return(base[c]); }
char cpbase(int c)
{ static char base[6] = "ACGT..";
if (c < Adenine) return('#');
if (c > NOBASE) return((char)c);
return(base[c]); }
char *aa(int *anticodon, csw *sw)
{ int p1,p2,p3;
if ((p1 = *anticodon) >= AMBIG) return(ambig_aaname);
if ((p2 = anticodon[1]) >= AMBIG) return(ambig_aaname);
if ((p3 = anticodon[2]) >= AMBIG) return(ambig_aaname);
return(aaname[aamap[sw->geneticcode][(p1<<4) + (p2<<2) + p3]]); }
char *translate(int *codon, csw *sw)
{ int p1,p2,p3,aa;
if ((p1 = *codon) >= AMBIG) return(ambig_aaname);
if ((p2 = codon[1]) >= AMBIG) return(ambig_aaname);
if ((p3 = codon[2]) >= AMBIG) return(ambig_aaname);
aa = aamap[sw->geneticcode][((3-p3)<<4)+((3-p2)<<2)+(3-p1)];
if ((aa == SeC) || (aa == Pyl)) aa = Stop;
return(aaname[aa]); }
char ltranslate(int *codon, gene *t, csw *sw)
{ int code,p1,p2,p3;
if (t->genetype == CDS) code = t->asst;
else code = sw->geneticcode;
if ((p1 = *codon) >= AMBIG) return(ambig_aaname[0]);
if ((p2 = codon[1]) >= AMBIG) return(ambig_aaname[0]);
if ((p3 = codon[2]) >= AMBIG) return(ambig_aaname[0]);
return(aaletter[aamap[code][((3-p3)<<4)+((3-p2)<<2)+(3-p1)]]); }
char ptranslate(int *codon, csw *sw)
{ int p1,p2,p3;
if ((p1 = *codon) >= AMBIG) return(ambig_aaname[0]);
if ((p2 = codon[1]) >= AMBIG) return(ambig_aaname[0]);
if ((p3 = codon[2]) >= AMBIG) return(ambig_aaname[0]);
return(aapolarity[aamap[sw->geneticcode][((3-p3)<<4)+((3-p2)<<2)+(3-p1)]]); }
double gc_content(gene *t)
{ int *s,*se;
double ngc;
static double score[6] = { 0.0,1.0,1.0,0.0,0.0,0.0 };
ngc = 0.0;
if ((t->nintron > 0) && (t->asst == 0))
{ s = t->eseq;
se = s + t->intron;
while (s < se) ngc += score[*s++];
s = se + t->nintron;
se = t->eseq + t->nbase + t->nintron;
while (s < se) ngc += score[*s++]; }
else
{ s = t->seq;
se = s + t->nbase;
while (s < se) ngc += score[*s++]; }
return(ngc/(double)t->nbase); }
void write_seq(FILE *f, int *seq, int newline)
{ int i,c;
i = 0;
while ((c = *seq++) >= Adenine)
{ fputc(cbase(c),f);
if (newline)
if (++i >= 50)
{ fputc('\n',f);
i = 0; }}
if (i > 0) fputc('\n',f); }
int find_var_hairpin(gene *t)
{ int e,stem,vstem,loop,*sn,*sen,*pos1,*pos2,*sb,*se,*sc,*sd,*sf,*s;
unsigned int c,cn,m;
static unsigned int A[6] = { 0,0,0x100,0x400,0,0 };
static unsigned int C[6] = { 0,0,0x400,0,0,0 };
static unsigned int G[6] = { 0x100,0x400,0,0x200,0,0 };
static unsigned int T[6] = { 0x400,0,0x200,0,0,0 };
static unsigned int te[6] = { 0,0,0,0,0,0 };
if (t->genetype != tRNA) return(0);
if (t->var < 13) return(0);
e = 0;
sb = t->seq + t->astem1 + t->spacer1 + 2*t->dstem + t->dloop +
t->spacer2 + 2*t->cstem + t->cloop + t->nintron;
sc = sb + 3; /* 4 */
se = sb + t->var - 2; /* 3 */
sf = se - 2;
te[0] = A[*se];
te[1] = C[*se];
te[2] = G[*se];
te[3] = T[*se];
while (--se > sf)
{ te[0] = (te[0] >> 4) | A[*se];
te[1] = (te[1] >> 4) | C[*se];
te[2] = (te[2] >> 4) | G[*se];
te[3] = (te[3] >> 4) | T[*se]; }
while (se >= sc)
{ te[0] = ((te[0] >> 4) | A[*se]);
te[1] = ((te[1] >> 4) | C[*se]);
te[2] = ((te[2] >> 4) | G[*se]);
te[3] = ((te[3] >> 4) | T[*se]);
s = se - 5;
sd = se - 7;
m = te[*s];
while (--s > sd) m = (m >> 4) + te[*s];
while (s >= sb)
{ m = (m >> 4) + te[*s];
c = m & 0xf;
if (c >= 9)
{ stem = 3;
loop = (int)(se - s) - 3;
sen = se;
sn = s + 2;
while (loop >= 6)
{ if ((cn = vbp[sen[-1]][sn[1]]) <= 0) break;
c += cn;
stem++;
loop -= 2;
sen--;
sn++; }
if (c > e)
{ e = c;
pos1 = s;
pos2 = sen;
vstem = stem; }}
s--; }
se--; }
if (e > 0)
return((((int)(pos1 - sb)) << 10) + (((int)(pos2 - sb)) << 5) + vstem);
else
return(0); }
void write_to_library(FILE *f, gene *t, csw *sw)
{ int *s;
static char trnatype[2][6] = { "tRNA","mtRNA" };
s = t->seq + t->anticodon;
fprintf(f,">%s",t->name);
if (!softstrpos(t->name,"RNA"))
switch (t->genetype)
{ case CDS:
fprintf(f," CDS");
break;
case srpRNA:
fprintf(f," srpRNA");
break;
case tmRNA:
if (t->asst > 0) fprintf(f," Permuted");
fprintf(f," tmRNA");
break;
case tRNA:
default:
t->varbp = find_var_hairpin(t);
if (t->tstem == 0) fprintf(f," TV-loop");
else if (t->dstem == 0) fprintf(f," D-loop");
switch(t->cloop)
{ case 6:
fprintf(f," %s-?""?""?(%c%c)",trnatype[sw->mtrna],
cbase(*s),cbase(*(s+1)));
break;
case 8:
fprintf(f," %s-?""?""?(%c%c%c%c)",trnatype[sw->mtrna],
cbase(*s),cbase(s[1]),cbase(s[2]),cbase(s[3]));
break;
case 7:
default:
fprintf(f," %s-%s(%c%c%c)",trnatype[sw->mtrna],
aa(s,sw),cbase(*s),cbase(*(s+1)),cbase(*(s+2)));
break; }
break; }
if (strpos(t->name,"bases)"))
fprintf(f,"\n");
else
fprintf(f," (%d bases)\n",t->nbase);
fprintf(f,"sequence =\n");
write_seq(f,t->seq,1);
if (*t->eseq >= Adenine)
{ fprintf(f,"extended sequence =\n");
write_seq(f,t->eseq,1); }
fprintf(f,"nbase = %d\n",t->nbase);
fprintf(f,"sense = %d\n",t->comp);
fprintf(f,"start = %ld\n",t->start);
fprintf(f,"stop = %ld\n",t->stop);
fprintf(f,"astem1 = %d\n",t->astem1);
fprintf(f,"astem2 = %d\n",t->astem2);
fprintf(f,"atail = %d\n",t->aatail);
fprintf(f,"spacer1 = %d\n",t->spacer1);
fprintf(f,"spacer2 = %d\n",t->spacer2);
fprintf(f,"dstem = %d\n",t->dstem);
fprintf(f,"dloop = %d\n",t->dloop);
fprintf(f,"cstem = %d\n",t->cstem);
fprintf(f,"cloop = %d\n",t->cloop);
fprintf(f,"anticodon = %d\n",t->anticodon);
fprintf(f,"nintron = %d\n",t->nintron);
fprintf(f,"intron = %d\n",t->intron);
fprintf(f,"asst = %d",t->asst);
if (t->genetype == tmRNA)
if (t->asst > 0) fprintf(f," permuted");
fprintf(f,"\ntps = %d\n",t->tps);
fprintf(f,"tpe = %d\n",t->tpe);
fprintf(f,"var = %d\n",t->var);
fprintf(f,"varbp = %d,%d,%d\n",((t->varbp >> 10)&0x1f),
((t->varbp >> 5)&0x1f),(t->varbp&0x1f));
fprintf(f,"tstem = %d\n",t->tstem);
fprintf(f,"tloop = %d\n",t->tloop);
fprintf(f,"gc = %g\n\n",gc_content(t)); }
void init_tmrna(FILE *f, csw *sw)
{ int c,*s;
s = sw->tmrna_struct;
while ((c = *s++) != TERM) itmparam(cbase(c),f); }
int *make_tv(int *seq, char matrix[][MATY],
int *x, int *y, int orient, int tv)
{ int i,px,py,stem;
static int ux[4] = { 1,0,-1,0 };
static int uy[4] = { 0,1,0,-1 };
static int vx[4] = { 0,-1,0,1 };
static int vy[4] = { 1,0,-1,0 };
static int loopu[26][26] =
{ { 0 }, { 0 }, { 0 }, { 0 }, { 0 }, { 0 },
{ 1,1,1,0,0,-1,-1 },
{ 1,1,1,1,0,-1,-1,-1 },
{ 1,1,1,1,0,0,-1,-1,-1 },
{ 1,1,1,1,1,0,-1,-1,-1,-1 },
{ 1,1,1,1,1,0,0,-1,-1,-1,-1 },
{ 1,1,1,1,1,1,0,-1,-1,-1,-1,-1 },
{ 1,1,1,1,1,1,0,0,-1,-1,-1,-1,-1 },
{ 1,1,1,1,1,1,0,0,0,-1,-1,-1,-1,-1 },
{ 1,1,1,1,1,1,1,0,0,-1,-1,-1,-1,-1,-1 },
{ 1,1,1,1,1,1,1,0,0,0,-1,-1,-1,-1,-1,-1 },
{ 1,1,1,1,1,1,1,1,0,0,-1,-1,-1,-1,-1,-1,-1 },
{ 1,1,1,1,1,1,1,1,0,0,0,-1,-1,-1,-1,-1,-1,-1 },
{ 1,1,1,1,1,1,1,1,1,0,0,-1,-1,-1,-1,-1,-1,-1,-1 },
{ 1,1,1,1,1,1,1,1,1,0,0,0,-1,-1,-1,-1,-1,-1,-1,-1 },
{ 1,1,1,1,1,1,1,1,1,1,0,0,-1,-1,-1,-1,-1,-1,-1,-1,-1 },
{ 1,1,1,1,1,1,1,1,1,1,0,0,0,-1,-1,-1,-1,-1,-1,-1,-1,-1 },
{ 1,1,1,1,1,1,1,1,1,1,1,0,0,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1 },
{ 1,1,1,1,1,1,1,1,1,1,1,0,0,0,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1 },
{ 1,1,1,1,1,1,1,1,1,1,1,1,0,0,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1 },
{ 1,1,1,1,1,1,1,1,1,1,1,1,0,0,0,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1 } };
static int loopv[26][26] =
{ { 0 }, { 0 }, { 0 }, { 0 }, { 0 }, { 0 },
{ 0,1,1,1,1,1,1 },
{ -1,1,1,1,1,1,1,1 },
{ -1,1,1,1,1,1,1,1,0 },
{ -1,0,1,1,1,1,1,1,1,0 },
{ -1,0,1,1,1,1,1,1,1,0,0 },
{ -1,0,0,1,1,1,1,1,1,1,0,0 },
{ -1,0,0,1,1,1,1,1,1,1,0,0,0 },
{ -1,0,0,1,1,1,1,1,1,1,0,0,0,0 },
{ -1,0,0,1,1,1,1,1,1,1,0,0,0,0,0 },
{ -1,0,0,0,1,1,1,1,1,1,1,0,0,0,0,0 },
{ -1,0,0,0,1,1,1,1,1,1,1,0,0,0,0,0,0 },
{ -1,0,0,0,0,1,1,1,1,1,1,1,0,0,0,0,0,0 },
{ -1,0,0,0,0,1,1,1,1,1,1,1,0,0,0,0,0,0,0 },
{ -1,0,0,0,0,0,1,1,1,1,1,1,1,0,0,0,0,0,0,0 },
{ -1,0,0,0,0,0,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0 },
{ -1,0,0,0,0,0,0,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0 },
{ -1,0,0,0,0,0,0,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0,0 },
{ -1,0,0,0,0,0,0,0,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0,0 },
{ -1,0,0,0,0,0,0,0,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0,0,0 },
{ -1,0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,0,0,0,0,0,0,0,0,0,0 } };
px = *x;
py = *y;
stem = 0;
if (tv < 6)
{ px += ux[orient];
py += uy[orient];
i = 0;
while (i < tv)
{ px += vx[orient];
py += vy[orient];
matrix[px][py] = cbase(*seq++);
i++; }
py += (6-i)*vy[orient];
goto FN; }
if (tv > 25)
{ if (tv % 2)
stem = (tv - 25)/2;
else
stem = (tv - 24)/2;
tv = tv - 2*stem; }
i = 0;
while (i < stem)
{ px += ux[orient];
py += uy[orient];
matrix[px][py] = cbase(*seq++);
i++; }
i = 0;
while (i < tv)
{ px += ux[orient]*loopu[tv][i] + vx[orient]*loopv[tv][i];
py += uy[orient]*loopu[tv][i] + vy[orient]*loopv[tv][i];
matrix[px][py] = cbase(*seq++);
i++; }
px += ux[orient]*loopu[tv][i] + vx[orient]*loopv[tv][i];
py += uy[orient]*loopu[tv][i] + vy[orient]*loopv[tv][i];
i = 0;
while (i < stem)
{ matrix[px][py] = cbase(*seq++);
px -= (ux[orient]);
py -= (uy[orient]);
i++; }
FN:
*x = px;
*y = py;
return(seq); }
int base_match(char b1, char b2)
{ int i,s;
static char base1[11] = "acgtgtagtg";
static char base2[11] = "tgcatggatg";
static int score[11] = { 2,2,2,2,1,1,3,3,3,3 };
s = 0;
for (i = 0; i < 10; i++)
if (b1 == base1[i])
if (b2 == base2[i])
{ s = score[i];
break; }
return(s); }
int *make_clover(int *seq, int b, int e, int stemlength,
char matrix[][MATY], int *x, int *y, int orient)
{ int i,px,py,pxb,pyb,pxe,pye,l,xlg,xlgd,ylgh,ylg;
int *s,*se;
static int ux[9] = { 1,0,-1,0,0,1,1,-1,-1 };
static int uy[9] = { 0,1,0,-1,1,-1,1,1,-1 };
static int vx[9] = { 0,-1,0,1,1,1,1,-1,-1 };
static int vy[9] = { 1,0,-1,0,0,0,0,0,0 };
static int loopu[18][18] =
{ { -1 }, { 0,-1 }, { 0,0,-1 }, { 0,1,-1,-1 }, { 0,1,0,-1,-1 },
{ 0,1,0,0,-1,-1 }, { 0,1,1,0,-1,-1,-1 }, { 0,1,1,0,0,-1,-1,-1 },
{ 0,1,1,1,0,-1,-1,-1,-1 }, { 0,1,1,1,0,0,-1,-1,-1,-1 },
{ 0,1,1,1,0,0,0,-1,-1,-1,-1 },
{ 0,1,1,1,1,0,0,-1,-1,-1,-1,-1 },
{ 0,1,1,1,1,0,0,0,-1,-1,-1,-1,-1 },
{ 0,1,1,1,1,1,0,0,-1,-1,-1,-1,-1,-1 },
{ 0,1,1,1,1,1,0,0,0,-1,-1,-1,-1,-1,-1 },
{ 0,1,1,1,1,1,1,0,0,-1,-1,-1,-1,-1,-1,-1 },
{ 0,1,1,1,1,1,1,0,0,0,-1,-1,-1,-1,-1,-1,-1 },
{ 0,1,1,1,1,1,1,0,0,0,0,-1,-1,-1,-1,-1,-1,-1 } };
static int loopv[18][18] =
{ { 2 }, { 1,1 }, { 0,1,1 }, { -1,2,2,-1 }, { -1,1,1,2,-1 },
{ -1,1,1,1,1,-1 }, { -1,0,1,1,1,1,-1 }, { -1,0,1,1,1,1,0,-1 },
{ -1,0,1,1,1,1,0,0,-1 }, { -1,0,0,1,1,1,1,0,0,-1 },
{ -1,0,0,0,1,1,1,1,0,0,-1 },
{ -1,0,0,0,1,1,1,1,0,0,0,-1 },
{ -1,0,0,0,1,1,1,1,0,0,0,0,-1 },
{ -1,0,0,0,0,1,1,1,1,0,0,0,0,-1 },
{ -1,0,0,0,0,1,1,1,1,0,0,0,0,0,-1 },
{ -1,0,0,0,0,0,1,1,1,1,0,0,0,0,0,-1 },
{ -1,0,0,0,0,0,1,1,1,1,0,0,0,0,0,0,-1 },
{ -1,0,0,0,0,0,0,1,1,1,1,0,0,0,0,0,0,-1 } };
static int dloopu[18][18] =
{ { -1 }, { 0,-1 }, { 0,0,-1 }, { 0,1,-1,-1 }, { 0,1,0,-1,-1 },
{ 0,1,0,0,-1,-1 }, { 0,1,1,0,-1,-1,-1 }, { 0,1,1,0,0,-1,-1,-1 },
{ 0,1,1,0,0,0,-1,-1,-1 }, { 0,1,1,1,0,0,-1,-1,-1,-1 },
{ 0,1,1,1,0,0,0,-1,-1,-1,-1 },
{ 0,1,1,1,1,0,0,-1,-1,-1,-1,-1 },
{ 0,1,1,1,1,0,0,0,-1,-1,-1,-1,-1 },
{ 0,1,1,1,1,1,0,0,-1,-1,-1,-1,-1,-1 },
{ 0,1,1,1,1,1,0,0,0,-1,-1,-1,-1,-1,-1 },
{ 0,1,1,1,1,1,1,0,0,-1,-1,-1,-1,-1,-1,-1 },
{ 0,1,1,1,1,1,1,0,0,0,-1,-1,-1,-1,-1,-1,-1 },
{ 0,1,1,1,1,1,1,0,0,0,0,-1,-1,-1,-1,-1,-1,-1 } };
static int dloopv[18][18] =
{ { 2 }, { 1,1 }, { 0,1,1 }, { -1,2,2,-1 }, { -1,1,1,2,-1 },
{ -1,1,1,1,1,-1 }, { -1,0,1,1,1,1,-1 }, { -1,0,1,1,1,1,0,-1 },
{ -1,0,1,1,1,1,1,-1,-1 }, { -1,0,0,1,1,1,1,0,0,-1 },
{ -1,0,0,0,1,1,1,1,0,0,-1 },
{ -1,0,0,0,1,1,1,1,0,0,0,-1 },
{ -1,0,0,0,1,1,1,1,0,0,0,0,-1 },
{ -1,0,0,0,0,1,1,1,1,0,0,0,0,-1 },
{ -1,0,0,0,0,1,1,1,1,0,0,0,0,0,-1 },
{ -1,0,0,0,0,0,1,1,1,1,0,0,0,0,0,-1 },
{ -1,0,0,0,0,0,1,1,1,1,0,0,0,0,0,0,-1 },
{ -1,0,0,0,0,0,0,1,1,1,1,0,0,0,0,0,0,-1 } };
static char bond1[5] = " +!:";
static char bond2[5] = " +-.";
px = *x;
py = *y;
s = seq + b;
se = s + stemlength;
while (s < se)
{ matrix[px][py] = cbase(*s++);
px += ux[orient];
py += uy[orient]; }
l = e - b - 2*stemlength;
if (l < 0) l = 0;
if (l < 18)
{ i = 0;
if (orient == DOWN)
{ while (i < l)
{ px += ux[orient]*dloopu[l][i] + vx[orient]*dloopv[l][i];
py += uy[orient]*dloopu[l][i] + vy[orient]*dloopv[l][i];
matrix[px][py] = cbase(*s++);
i++; }
px += ux[orient]*dloopu[l][i] + vx[orient]*dloopv[l][i];
py += uy[orient]*dloopu[l][i] + vy[orient]*dloopv[l][i]; }
else
{ while (i < l)
{ px += ux[orient]*loopu[l][i] + vx[orient]*loopv[l][i];
py += uy[orient]*loopu[l][i] + vy[orient]*loopv[l][i];
matrix[px][py] = cbase(*s++);
i++; }
px += ux[orient]*loopu[l][i] + vx[orient]*loopv[l][i];
py += uy[orient]*loopu[l][i] + vy[orient]*loopv[l][i]; }}
else
{ ylgh = ((l >> 2) - 2) >> 1;
ylg = (ylgh << 1) + 2;
xlgd = l - ylg - 2*ylgh + 1;
xlg = (xlgd + 1) >> 1;
pxb = px - ylgh*vx[orient];
if ((pxb < 0) || (pxb >= MATX)) goto NOLOOP;
pyb = py - ylgh*vy[orient];
if ((pyb < 0) || (pyb >= MATY)) goto NOLOOP;
pxe = px + xlg*ux[orient] + (ylg - ylgh + 1)*vx[orient];
if ((pxe < 0) || (pxe >= MATX)) goto NOLOOP;
pye = py + xlg*uy[orient] + (ylg - ylgh + 1)*vy[orient];
if ((pye < 0) || (pye >= MATY)) goto NOLOOP;
for (i = 0; i < ylgh; i++)
{ px -= vx[orient];
py -= vy[orient];
matrix[px][py] = cbase(*s++); }
for (i = 0; i < xlg; i++)
{ px += ux[orient];
py += uy[orient];
matrix[px][py] = cbase(*s++); }
for (i = 1; i < ylg; i++)
{ px += vx[orient];
py += vy[orient];
matrix[px][py] = cbase(*s++); }
px += vx[orient];
py += vy[orient];
if (!(xlgd & 1)) matrix[px][py] = cbase(*s++);
for (i = 0; i < xlg; i++)
{ px -= ux[orient];
py -= uy[orient];
matrix[px][py] = cbase(*s++); }
for (i = 1; i < ylgh; i++)
{ px -= vx[orient];
py -= vy[orient];
matrix[px][py] = cbase(*s++); }
px -= (ux[orient] + vx[orient]);
py -= (uy[orient] + vy[orient]); }
goto STEMBOND;
NOLOOP:
px += ux[orient]*loopu[0][0] + vx[orient]*loopv[0][0];
py += uy[orient]*loopu[0][0] + vy[orient]*loopv[0][0];
STEMBOND:
se = seq + e;
s = se - stemlength;
while (s < se)
{ matrix[px][py] = cbase(*s++);
i = base_match(matrix[px][py],
matrix[px - 2*vx[orient]][py - 2*vy[orient]]);
switch(orient)
{ case RIGHT:
case LEFT: matrix[px - vx[orient]][py - vy[orient]] = bond1[i];
break;
case SLANTDR:
case SLANTUR:
case SLANTUL:
case SLANTDL:
case UPRIGHT:
case UP:
case DOWN: matrix[px - vx[orient]][py - vy[orient]] = bond2[i];
break; }
px -= ux[orient];
py -= uy[orient]; }
*x = px;
*y = py;
return(se); }
int *make_dv(int *seq, char matrix[][MATY], int dloop,
int orient, int *xp, int *yp)
{ int i,x,y;
static int ux[5] = { 1,0,-1,0,0 };
static int uy[5] = { 0,1,0,-1,1 };
static int vx[5] = { 0,-1,0,1,1 };
static int vy[5] = { 1,0,-1,0,0 };
static int loopu[22][22] =
{ { -1 }, { -1,0 },
{ -1,-1,1 },
{ -1,-1,0,1 },
{ -1,-1,0,0,1 },
{ -1,-1,-1,0,1,1 },
{ -1,-1,-1,0,0,1,1 },
{ -1,-1,-1,-1,0,1,1,1 },
{ -1,-1,-1,-1,0,0,1,1,1 },
{ -1,-1,-1,-1,-1,0,1,1,1,1 },
{ -1,-1,-1,-1,-1,0,0,1,1,1,1 },
{ -1,-1,-1,-1,-1,-1,0,1,1,1,1,1 },
{ -1,-1,-1,-1,-1,-1,0,0,1,1,1,1,1 },
{ -1,-1,-1,-1,-1,-1,-1,0,1,1,1,1,1,1 },
{ -1,-1,-1,-1,-1,-1,0,-1,0,1,1,1,1,1,1 },
{ -1,-1,-1,-1,-1,-1,-1,-1,0,1,1,1,1,1,1,1 },
{ -1,-1,-1,-1,-1,-1,-1,-1,0,0,1,1,1,1,1,1,1 },
{ -1,-1,-1,-1,-1,-1,-1,-1,-1,0,1,1,1,1,1,1,1,1 },
{ -1,-1,-1,-1,-1,-1,-1,-1,-1,0,0,1,1,1,1,1,1,1,1 },
{ -1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,1,1,1,1,1,1,1,1,1 },
{ -1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,0,1,1,1,1,1,1,1,1,1 },
{ -1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,1,1,1,1,1,1,1,1,1,1 } };
static int loopv[22][22] =
{ { -6 }, { -3,-3 },
{ -2,-2,-2 },
{ -2,-1,-1,-2 },
{ -1,-1,-2,-1,-1 },
{ -1,-1,-1,-1,-1,-1 },
{ 0,-1,-1,-1,-1,-1,-1 },
{ 0,-1,0,-1,-1,-1,-1,-1 },
{ 0,-1,0,-1,-1,-1,0,-1,-1 },
{ 0,0,-1,0,-1,-1,-1,0,-1,-1 },
{ 0,0,-1,0,-1,-1,-1,0,-1,0,-1 },
{ 0,0,0,-1,0,-1,-1,-1,0,-1,0,-1 },
{ 0,0,0,-1,0,-1,-1,-1,0,-1,0,0,-1 },
{ 0,0,0,0,-1,0,-1,-1,-1,0,-1,0,0,-1 },
{ 0,0,0,0,-1,0,-1,-1,-1,0,-1,0,0,0,-1 },
{ 0,0,0,0,0,-1,0,-1,-1,-1,0,-1,0,0,0,-1 },
{ 0,0,0,0,0,-1,0,-1,-1,-1,-1,0,0,0,0,0,-1 },
{ 0,0,0,0,0,0,-1,0,-1,-1,-1,0,-1,0,0,0,0,-1 },
{ 0,0,0,0,0,0,-1,0,-1,-1,-1,-1,0,0,0,0,0,0,-1 },
{ 0,0,0,0,0,0,0,-1,0,-1,-1,-1,0,-1,0,0,0,0,0,-1 },
{ 0,0,0,0,0,0,0,-1,0,-1,-1,-1,-1,0,0,0,0,0,0,0,-1 },
{ 0,0,0,0,0,0,0,0,-1,0,-1,-1,-1,0,-1,0,0,0,0,0,0,-1 } };
x = *xp;
y = *yp;
if ((dloop < 2) || (dloop > 21))
{ x--;
y-= 6;
seq += dloop;
goto FN; }
i = 0;
while (i < dloop)
{ x += ux[orient]*loopu[dloop][i] + vx[orient]*loopv[dloop][i];
y += uy[orient]*loopu[dloop][i] + vy[orient]*loopv[dloop][i];
matrix[x][y] = cbase(*seq++);
i++; }
x += ux[orient]*loopu[dloop][i] + vx[orient]*loopv[dloop][i];
y += uy[orient]*loopu[dloop][i] + vy[orient]*loopv[dloop][i];
FN:
*xp = x;
*yp = y;
return(seq); }
int *make_var(int *seq, char matrix[][MATY],
int *x, int *y, int orient, int var, int varbp)
{ int i,b,e,p,px,py,pxf,pyf,l,stem;
static int ux[4] = { 1,0,-1,0 };
static int uy[4] = { 0,1,0,-1 };
static int vx[4] = { 0,-1,0,1 };
static int vy[4] = { 1,0,-1,0 };
static int preu[4][5][4] =
{ { {0},{1},{1},{1},{1} },
{ {0},{1,1},{1,1},{1,1},{1,1} },
{ {0},{0,1,1},{0,1,1},{1,1,1},{1,1,1} },
{ {0},{0,0,1,1},{0,0,1,1},{0,1,1,1},{0,1,1,1} } };
static int prev[4][5][4] =
{ { {0},{0},{0},{0},{-1} },
{ {0},{0,1},{0,0},{-1,0},{-1,0} },
{ {0},{0,1,0},{0,0,0},{-1,0,0},{-1,0,-1} },
{ {0},{0,1,0,0},{0,1,0,-1},{0,0,0,-1},{0,0,-1,-1} } };
static int postu[4][5][4] =
{ { {0},{0},{1,-1},{0,-1,0},{1,-1,-1,0} },
{ {0},{0},{0,-1},{0,-1,0},{0,-1,-1,0} },
{ {0},{0},{0,-1},{0,-1,-1},{1,-1,-1,-1} },
{ {0},{0},{0,-1},{0,-1,-1},{1,-1,-1,-1} } };
static int postv[4][5][4] =
{ { {0},{0},{0,1},{0,1,1},{0,1,1,1} },
{ {0},{0},{0,1},{0,1,1},{0,1,1,1} },
{ {0},{0},{0,1},{0,1,1},{0,1,1,1} },
{ {0},{0},{0,1},{0,1,1},{0,1,1,1} } };
static int loopu[10][10] =
{ { 2 }, { 1,1 }, { 1,1,0 }, { 1,0,1,0 }, { 1,1,0,0,0 },
{ 1,1,1,-1,-1,1 }, { 1,1,1,0,0,-1,0 }, { 1,1,1,1,0,-1,-1,0 },
{ 1,1,1,1,0,0,-1,-1,0 }, { 1,1,1,1,1,0,-1,-1,-1,0 } };
static int loopv[10][10] =
{ { 3 }, { 1,2 }, { 0,1,2 }, { 0,1,1,1 }, { -1,1,1,1,1 },
{ -1,0,1,1,1,1 }, { -1,-1,1,1,1,1,1 }, { -1,-1,0,1,1,1,1,1 },
{ -1,-1,-1,1,1,1,1,1,1 }, { -1,-1,-1,0,1,1,1,1,1,1 } };
px = *x;
py = *y;
if (var < 0) var = 0;
if (var > 30) var = 30;
if (varbp > 0)
{ b = (varbp >> 10) & 0x1f;
if (b > 3) goto NBP;
stem = varbp & 0x1f;
e = stem + ((varbp >> 5) & 0x1f);
p = var - e;
if (p < 1) goto NBP; /* 2 */
if (p > 4) goto NBP;
pxf = px + 2*ux[orient] + 3*vx[orient];
pyf = py + 2*uy[orient] + 3*vy[orient];
i = 0;
while (i < b)
{ px += ux[orient]*preu[b][p][i] + vx[orient]*prev[b][p][i];
py += uy[orient]*preu[b][p][i] + vy[orient]*prev[b][p][i];
matrix[px][py] = cbase(*seq++);
i++; }
px += ux[orient]*preu[b][p][b] + vx[orient]*prev[b][p][b];
py += uy[orient]*preu[b][p][b] + vy[orient]*prev[b][p][b];
seq = make_clover(seq,0,e-b,stem,matrix,&px,&py,orient+SLANT);
i = 0;
while (i < p)
{ px += ux[orient]*postu[b][p][i] + vx[orient]*postv[b][p][i];
py += uy[orient]*postu[b][p][i] + vy[orient]*postv[b][p][i];
matrix[px][py] = cbase(*seq++);
i++; }
*x = pxf;
*y = pyf;
goto FIN; }
NBP:
if (var > 9)
{ if (var % 2) stem = (var - 7)/2;
else stem = (var - 6)/2; }
else stem = 0;
l = var - 2*stem;
i = 0;
while (i < stem)
{ px += ux[orient] - vx[orient];
py += uy[orient] - vy[orient];
matrix[px][py] = cbase(*seq++);
i++; }
i = 0;
while (i < l)
{ px += ux[orient]*loopu[l][i] + vx[orient]*loopv[l][i];
py += uy[orient]*loopu[l][i] + vy[orient]*loopv[l][i];
matrix[px][py] = cbase(*seq++);
i++; }
px += ux[orient]*loopu[l][i] + vx[orient]*loopv[l][i];
py += uy[orient]*loopu[l][i] + vy[orient]*loopv[l][i];
i = 0;
while (i < stem)
{ matrix[px][py] = cbase(*seq++);
px -= (ux[orient] - vx[orient]);
py -= (uy[orient] - vy[orient]);
i++; }
*x = px;
*y = py;
FIN:
return(seq); }
void remove_inserts(int *s1, int *s2)
{ int flag,c;
flag = 0;
while ((c = *s1++) != TERM)
{ if (c == INSERT)
{ flag = 1 - flag;
continue; }
if (flag) continue;
*s2++ = c; }
*s2 = TERM; }
void build_trna(gene *t, char matrix[][MATY], int x, int y, csw *sw)
{ int i,j,e,c,*seq;
int rseq[150];
static char bond2[5] = " +-.";
t->varbp = find_var_hairpin(t);
remove_inserts(t->seq,rseq);
seq = rseq;
i = 0;
while (i < t->astem1)
{ matrix[x][y] = cbase(*seq++);
y--;
i++; }
if (t->spacer1 > 0)
{ x--;
if (t->spacer1 >= 3) matrix[x][y+1] = cbase(*seq++);
matrix[x][y] = cbase(*seq++);
y--;
x--;
if (t->spacer1 >= 2) matrix[x][y] = cbase(*seq++);
if ((t->spacer2 < 2) || (t->spacer1 > 1))
{ x--;
y--; }}
if (t->dstem > 0)
{ e = 2*t->dstem + t->dloop;
seq = make_clover(seq,0,e,t->dstem,matrix,&x,&y,LEFT);
if (t->spacer2 > 1) x--;
y--;
if (t->spacer2 > 0) matrix[x][y] = cbase(*seq++);
y--;
if (t->spacer2 > 1)
{ if (t->spacer1 > 1) x++;
matrix[x][y] = cbase(*seq++);
if (t->spacer1 < 2) y--; }
x++; }
else
seq = make_dv(seq,matrix,t->dloop,RIGHT,&x,&y);
e = 2*t->cstem + t->cloop;
seq = make_clover(seq,0,e,t->cstem,matrix,&x,&y,DOWN);
if (t->tstem > 0)
{ seq = make_var(seq,matrix,&x,&y,RIGHT,t->var,t->varbp);
e = 2*t->tstem + t->tloop;
seq = make_clover(seq,0,e,t->tstem,matrix,&x,&y,RIGHT);
y++; }
else
seq = make_tv(seq,matrix,&x,&y,RIGHT,t->tloop);
e = t->astem2;
i = 0;
while (i < e)
{ if ((c = *seq++) < Adenine) break;
matrix[x][y] = cbase(c);
j = base_match(matrix[x][y],matrix[x - 2][y]);
matrix[x - 1][y] = bond2[j];
y++;
i++; }
i = 0;
e = (sw->aataildisp)?ASTEM2_EXTD:t->aatail;
j = (e < 2)?e:2;
while (i < j)
{ if ((c = *seq++) < Adenine) break;
matrix[x][y] = cbase(c);
x++;
y++;
i++; }
e -= j;
i = 0;
while (i < e)
{ if ((c = *seq++) < Adenine) break;
matrix[x][y] = cbase(c);
x++;
i++; }}
void build_tmrna(gene *t, char matrix[][MATY], int x, int y, csw *sw)
{ int i,j,e,c,tarm,*seq;
int rseq[2*MAXTMRNALEN+1];
static char bond2[5] = " +-.";
remove_inserts(t->eseq,rseq);
seq = rseq + t->asst;
i = 0;
while (i < t->astem1)
{ matrix[x][y] = cbase(*seq++);
y--;
i++; }
seq = make_dv(seq,matrix,t->dloop,RIGHT,&x,&y);
tarm = 2*t->tstem + t->tloop;
e = (t->asst > 0)?
(t->cstem - t->dloop - t->astem1 - t->asst + 54):
(2*t->cstem + t->cloop + t->nintron);
seq = make_clover(seq,0,e,t->cstem,matrix,&x,&y,DOWN);
seq = make_var(seq,matrix,&x,&y,RIGHT,t->var,t->varbp);
seq = make_clover(seq,0,tarm,t->tstem,matrix,&x,&y,RIGHT);
y++;
e = t->astem2;
i = 0;
while (i < e)
{ if ((c = *seq++) == TERM) break;
matrix[x][y] = cbase(c);
j = base_match(matrix[x][y],matrix[x - 2][y]);
matrix[x - 1][y] = bond2[j];
y++;
i++; }
e = (sw->aataildisp)?ASTEM2_EXTD:t->aatail;
j = (e < 2)?e:2;
i = 0;
while (i < j)
{ if ((c = *seq++) == TERM) break;
matrix[x][y] = cbase(c);
x++;
y++;
i++; }
e -= j;
i = 0;
while (i < e)
{ if ((c = *seq++) == TERM) break;
matrix[x][y] = cbase(c);
x++;
i++; } }
void init_matrix(char matrix[][MATY])
{ int i,j;
for (i =0; i < MATY; i++)
for (j = 0; j < MATX; j++) matrix[j][i] = ' '; }
void disp_matrix(FILE *f, char matrix[][MATY], int ylines)
{ int i,j,k;
i = ylines;
while (--i >= 0)
{ k = MATX;
while (--k > 0) if (matrix[k][i] != ' ') break;
for (j = 0; j <= k; j++) fputc(matrix[j][i],f);
fputc('\n',f); }
fputc('\n',f); }
void xcopy(char m[][MATY], int x, int y, char *s, int l)
{ int i;
char c;
i = 0;
while (i < l)
{ if (x >= MATX) break;
if (!(c = *s++)) break;
m[x++][y] = c;
i++; }}
int identify_tag(char tag[], int len, char (*thit)[50], int nt)
{ int i,n;
char *s,*st,*sb,*sd;
static struct { char name[50]; char tag[50]; } tagdatabase[NTAG] =
{ { "Cyanidioschyzon merolae Chloroplast","ANQILPFSIPVKHLAV" },
{ "Mesostigma viride chloroplast","ANNILPFNRKTAVAV" },
{ "Nephroselmis olivacea chloroplast","TTYHSCLEGHLS" },
{ "Pirellula sp.","AEENFALAA" },
{ "Rhodopirellula baltica","AEENFALAA" },
{ "Desulfotalea psychrophila","ADDYNYAVAA" },
{ "Desulfuromonas acetoxidans","ADTDVSYALAA" },
{ "Exiguobacterium sp.","GKTNTQLAAA" },
{ "Mycoplasma gallisepticum","DKTSKELADENFVLNQLASNNYALNF" },
{ "Aquifex aeolicus","APEAELALAA" },
{ "Thermotoga maritima ","ANEPVAVAA" },
{ "Thermotoga neapolitana","ANEPVAVAA" },
{ "Chloroflexus aurantiacus","ANTNTRAQARLALAA" },
{ "Thermus thermophilus","ANTNYALAA" },
{ "Deinococcus radiodurans","GNQNYALAA" },
{ "Deinococcus geothermalis","GNQNYALAA" },
{ "Cytophaga hutchinsonii","GEESYAMAA" },
{ "Bacteroides fragilis","GETNYALAA" },
{ "Tannerella forsythensis","GENNYALAA" },
{ "Porphyromonas gingivalis","GENNYALAA" },
{ "Prevotella intermedia","GENNYALAA" },
{ "Chlorobium tepidum","ADDYSYAMAA" },
{ "Chlorobium chlorochromatii","ADDYSYAMAA" },
{ "Salinibacter ruber","ADDYSYAMAA" },
{ "Gemmata obscuriglobus","AEPQYSLAA" },
{ "Chlammydophila pneumoniae","AEPKAECEIISLFDSVEERLAA" },
{ "Chlammydophila caviae","AEPKAECEIISFSDLTEERLAA" },
{ "Chlammydophila abortus","AEPKAKCEIISFSELSEQRLAA" },
{ "Chlammydia trachomatis","AEPKAECEIISFADLEDLRVAA" },
{ "Chlammydia muridarum","AEPKAECEIISFADLNDLRVAA" },
{ "Nostoc PCC7120","ANNIVKFARKDALVAA" },
{ "Nostoc punctiforme","ANNIVNFARKDALVAA" },
{ "Fremyella diplosiphon","ANNIVKFARKEALVAA" },
{ "Plectonema boryanum","ANNIVPFARKTAPVAA" },
{ "Trichodesmium erythraeum","ANNIVPFARKQVAALA" },
{ "Oscillatoria 6304","ANNIVPFARKAAPVAA" },
{ "Chroococcidiopsis PCC6712","ANNIVKFERQAVFA" },
{ "Synechocystis PCC6803","ANNIVSFKRVAIAA" },
{ "Thermosynechococcus elongatus","ANNIVPFARKAAAVA" },
{ "Synechococcus PCC6301","ANNIVPFARKAAPVAA" },
{ "Synechococcus elongatus","ANNIVPFARKAAPVAA" },
{ "Synechococcus WH8102","ANNIVRFSRHAAPVAA" },
{ "Synechococcus PCC6307","ANNIVRFSRQAAPVAA" },
{ "Synechococcus PCC7002","ANNIVPFARKAAAVA" },
{ "Synechococcus PCC7009","ANNIVRFSRQAAPVAA" },
{ "Synechococcus PCC6904","ANNIVRFSRQAAPVAA" },
{ "Synechococcus CC9311","ANNIVRFSRQAAPVAA" },
{ "Synechococcus CC9902","ANNIVRFSRQAAPVAA" },
{ "Synechococcus CC9605","ANNIVRFSRQAAPVAA" },
{ "Prochlorococcus marinus 1","ANKIVSFSRQTAPVAA" },
{ "Prochlorococcus marinus 2","ANNIVRFSRQPALVAA" },
{ "Prochlorococcus marinus 3","ANKIVSFSRQTAPVAA" },
{ "Cyanophora paradoxa chloroplast","ATNIVRFNRKAAFAV" },
{ "Thalassiosira weissflogii chloroplast","ANNIIPFIFKAVKTKKEAMALNFAV" },
{ "Odontella sinensis chloroplast","ANNLISSVFKSLSTKQNSLNLSFAV" },
{ "Bolidomonas pacifica chloroplast","ANNILAFNRKSLSFA" },
{ "Pavlova lutheri chloroplast","ANNILSFNRVAVA" },
{ "Porphyra purpurea chloroplast","AENNIIAFSRKLAVA" },
{ "Guillardia theta chloroplast","ASNIVSFSSKRLVSFA" },
{ "Fibrobacter succinogenes","ADENYALAA" },
{ "Treponema pallidum","ANSDSFDYALAA" },
{ "Treponema denticola","AENNDSFDYALAA" },
{ "Leptospira interrogans","ANNELALAA" },
{ "Borrelia burgdorferi","AKNNNFTSSNLVMAA" },
{ "Borrelia garinii","AKNNNFTSSNLVMAA" },
{ "Caulobacter crescentus","ANDNFAEEFAVAA" },
{ "Rhodobacter sphaeroides","ANDNRAPVALAA" },
{ "Silicibacter pomeroyi","ANDNRAPVALAA" },
{ "Silicibacter TM1040","ANDNRAPVALAA" },
{ "Paracoccus denitrificans","ANDNRAPVALAA" },
{ "Nitrobacter hamburgensis","ANDNYAPVAQAA" },
{ "Nitrobacter winogradskyi","ANDNYAPVAQAA" },
{ "Nitrobacter Nb-311A","ANDNYAPVAQAA" },
{ "Rhodopseudomonas palustris","ANDNYAPVAQAA" },
{ "Rhodopseudomonas palustris 4","ANDNVRMNEVRLAA" },
{ "Bradyrhizobium japonicum","ANDNFAPVAQAA" },
{ "Agrobacterium tumefaciens 1","ANDNNAKEYALAA" },
{ "Agrobacterium tumefaciens 2","ANDNNAKECALAA" },
{ "Rhizobium leguminosarum","ANDNYAEARLAA" },
{ "Sinorhizobium meliloti","ANDNYAEARLAA" },
{ "Mesorhizobium loti","ANDNYAEARLAA" },
{ "Mesorhizobium sp.","ANDNYAEARLAA" },
{ "Bartonella henselae","ANDNYAEARLAA" },
{ "Bartonella quintana","ANDNYAEARLAA" },
{ "Brucella melitensis","ANDNNAQGYALAA" },
{ "Brucella abortus","ANDNNAQGYALAA" },
{ "Brucella suis","ANDNNAQGYALAA" },
{ "Methylobacterium extorquens","ANDNFAPVAVAA" },
{ "Magnetospirillum magnetotacticum 1","ANDNFAPVAVAA" },
{ "Magnetospirillum magnetotacticum 2","ANDNVELAAAA" },
{ "Rhodospirillum rubrum","ANDNVELAAAA" },
{ "Novosphingobium aromaticivorans","ANDNEALALAA" },
{ "Sphingopyxis alaskensis","ANDNEALALAA" },
{ "Erythrobacter litoralis","ANDNEALALAA" },
{ "Ehrlichia chaffeensis","ANDNFVFANDNNSSANLVAA" },
{ "Anaplasma phagocytophilum","ANDDFVAANDNVETAFVAAA" },
{ "Wolbachi.sp","ANDNFAAEDNVDAIAA" },
{ "Rickettsia conorii","ANDNNRSVGHLALAA" },
{ "Rickettsia sibirica","ANDNNRSVGHLALAA" },
{ "Rickettsia typhi","ANDNKRYVGVAALAAA" },
{ "Rickettsia prowazekii","ANDNRYVGVPALAAA" },
{ "Neisseria gonorrhoeae","ANDETYALAA" },
{ "Neisseria meningitidis","ANDETYALAA" },
{ "Neisseria lactamica","ANDETYALAA" },
{ "Chromobacterium violaceum","ANDETYALAA" },
{ "Uncultured U02","ANDEQFALAA" },
{ "Nitrosomonas europaea","ANDENYALAA" },
{ "Nitrosomonas cryotolerans","ANDENYALAA" },
{ "Methylobacillus glycogenes","ANDETYALAA" },
{ "Methylobacillus flagellatus","ANDETYALAA" },
{ "Moraxella catarrhalis","ANDETYALAA" },
{ "Uncultured U04","ANDETYALAA" },
{ "Ralstonia pickettii","ANDERYALAA" },
{ "Ralstonia solanacearum","ANDNRYQLAA" },
{ "Ralstonia eutropha","ANDERYALAA" },
{ "Ralstonia metallidurans","ANDERYALAA" },
{ "Alcaligenes faecalis","ANDERFALAA" },
{ "Comamonas testosteroni","ANDERFALAA" },
{ "Variovorax paradoxus","ANDERFALAA" },
{ "Hydrogenophaga palleronii","ANDERFALAA" },
{ "Burkholderia pseudomallei","ANDDTFALAA" },
{ "Burkholderia mallei","ANDDTFALAA" },
{ "Burkholderia fungorum","ANDDTFALAA" },
{ "Burkholderia cepacia","ANDDTFALAA" },
{ "Burkholderia cenocepacia","ANDDTFALAA" },
{ "Burkholderia thailandensis","ANDDTFALAA" },
{ "Burkholderia vietnamiensis","ANDDTFALAA" },
{ "Burkholderia sp. 383","ANDDTFALAA" },
{ "Bordetella avium","ANDERFALAA" },
{ "Bordetella pertussis","ANDERFALAA" },
{ "Bordetella parapertussis","ANDERFALAA" },
{ "Bordetella bronchiseptica","ANDERFALAA" },
{ "Polaromonas JS666","ANDERFALAA" },
{ "Rubrivivax gelatinosus","ANDERFALAA" },
{ "Uncultured stronglyoides1","ANDERFALAA" },
{ "Azoarcus BH72","ANDERFALAA" },
{ "Xylella fastidiosa 1","ANEDNFAVAA" },
{ "Xylella fastidiosa 2","ANEDNFALAA" },
{ "Xylella fastidiosa 3","ANEDNFAIAA" },
{ "Xylella fastidiosa 4","ANEDNFALAA" },
{ "Xanthomonas campestris 1","ANDDNYGSDFAIAA" },
{ "Xanthomonas campestris 2","ANDDNYGSDSAIAA" },
{ "Xanthomonas axonopodis","ANDDNYGSDFAIAA" },
{ "Xanthomonas oryzae","ANDDNYGSDFAIAA" },
{ "Legionella pneumophila","ANDENFAGGEAIAA" },
{ "Coxiella burnetii","ANDSNYLQEAYA" },
{ "Methylococcus capsulatus","ANDDVYALAA" },
{ "Uncultured U01a","ANDSNYALAA" },
{ "Dichelobacter nodosus","ANDDNYALAA" },
{ "Francisella tularensis 1","GNKKANRVAANDSNFAAVAKAA" },
{ "Francisella tularensis 2","ANDSNFAAVAKAA" },
{ "Acidithiobacillus ferrooxidans","ANDSNYALAA" },
{ "Acinetobacter ADP1","ANDETYALAA" },
{ "Psychrobacter 2734","ANDENYALAA" },
{ "Psychrobacter cryohalolentis","ANDENYALAA" },
{ "Psychrobacter arcticus","ANDENYALAA" },
{ "Azotobacter vinelandii","ANDDNYALAA" },
{ "Pseudomonas aeruginosa","ANDDNYALAA" },
{ "Pseudomonas syringae 1","ANDENYGAQLAA" },
{ "Pseudomonas syringae 2","ANDETYGEYALAA" },
{ "Pseudomonas syringae 3","ANDENYGAQLAA" },
{ "Pseudomonas fluorescens 1","ANDDQYGAALAA" },
{ "Pseudomonas fluorescens 2","ANDENYGQEFALAA" },
{ "Pseudomonas putida 1","ANDENYGAEYKLAA" },
{ "Marinobacter hydrocarbonoclasticus","ANDENYALAA" },
{ "Marinobacter aquaeolei","ANDENYALAA" },
{ "Pseudoalteromonas haloplanktis","ANDDNYSLAA" },
{ "Pseudoalteromonas atlantica","ANDENYALAA" },
{ "Uncultured WW11","ANDDNYALAA" },
{ "Shewanella oneidensis","ANDDNYALAA" },
{ "Shewanella putrefaciens","ANDDNYALAA" },
{ "Shewanella PV-4","ANDDNYALAA" },
{ "Shewanella amazonensis","ANDDNYALAA" },
{ "Shewanella SAR-1","ANDDNYALAA" },
{ "Shewanella ANA-3","ANDDNYALAA" },
{ "Idiomarina loihiensis","ANDDNYALAA" },
{ "Photorhabdus asymbiotica","ANDNEYALVA" },
{ "Microbulbifer degradans","ANDDNYGAQLAA" },
{ "Saccharophagus degradans","ANDDNYGAQLAA" },
{ "Colwellia sp","ANDDTFALAA" },
{ "Colwellia psychrerythraea","ANDDTFALAA" },
{ "Photobacterium phosphoreum","ANDENYALAA" },
{ "Vibrio cholerae","ANDENYALAA" },
{ "Vibrio vulnificus","ANDENYALAA" },
{ "Vibrio Ex25","ANDENYALAA" },
{ "Vibrio parahemolyticus","ANDENYALAA" },
{ "Aeromonas salmonicida","ANDENYALAA" },
{ "Aeromonas hydrophila 1","ANDENYALAA" },
{ "Aeromonas hydrophila 2","ANDENYALAA" },
{ "Uncultured VLW3","ANDENYALAA" },
{ "Uncultured VLS13","ANDENYALAA" },
{ "Uncultured WW9","ANDENYALAA" },
{ "Uncultured WW10","ANDENYALAV" },
{ "Uncultured VLW5","ANDENYALAA" },
{ "Uncultured RCA4","ANDETYALAA" },
{ "Uncultured LEM1","ANDETYALAA" },
{ "Uncultured LEM2","ANDETHALAA" },
{ "Wigglesworthia brevipalpis","AKHKYNEPALLAA" },
{ "Wigglesworthia glossinidia","AKHKYNEPALLAA" },
{ "Buchnera aphidicola 1","ANNKQNYALAA" },
{ "Buchnera aphidicola 2","ANNKQNYALAA" },
{ "Buchnera aphidicola 3","AKQNQYALAA" },
{ "Shigella dysenteriae 1","ANDENYALAA" },
{ "Shigella dysenteriae 2","ANDENYALAA" },
{ "Shigella flexneri","ANDENYALAA" },
{ "Shigella boydii","ANDENYALAA" },
{ "Shigella sonnei","ANDENYALAA" },
{ "Escherichia coli","ANDENYALAA" },
{ "Providencia rettgeri","ANDENYALAA" },
{ "Serratia marcescens","ANDENYALAA" },
{ "Klebsiella pneumoniae","ANDENYALAA" },
{ "Pectobacterium carotovora","ANDENYALAA" },
{ "Erwinia chrysanthemi","ANDENFAPAALAA" },
{ "Erwinia amylovora","ANDENFAPAALAA" },
{ "Erwinia carotovora","ANDENYALAA" },
{ "Salmonella bongori","ANDENYALAA" },
{ "Salmonella typhimurium","ANDETYALAA" },
{ "Salmonella typhi","ANDETYALAA" },
{ "Salmonella paratyphi","ANDENYALAA" },
{ "Salmonella enterica 1","ANDETYALAA" },
{ "Salmonella enterica 2","ANDENYALAA" },
{ "Salmonella enterica 3","ANDETYALAA" },
{ "Salmonella enterica 5","ANDETYALAA" },
{ "Salmonella enterica 6","ANDENYALAA" },
{ "Uncultured RCA1","ANDENYALAA" },
{ "Uncultured VLS1","ANDENYALAA" },
{ "Uncultured WW1","ANDENYALAA" },
{ "Uncultured RCA2","SNDENYALAA" },
{ "Uncultured WW2","ANDENYALAA" },
{ "Uncultured QL1","ANVENYALAA" },
{ "Uncultured WW4","ANDGNYALAA" },
{ "Uncultured VLS5","ANDETYALAA" },
{ "Uncultured FS1","ANDETYALAA" },
{ "Uncultured VLS6","ANDENYALAA" },
{ "Uncultured FS2","ANDENYALAA" },
{ "Uncultured WW5","ANDENYALAA" },
{ "Uncultured VLW1","ANDENYALAA" },
{ "Uncultured VLS7","ANDENYALAA" },
{ "Uncultured VLS9","ANDENYALAA" },
{ "Uncultured VLW2","ANDENYALAA" },
{ "Uncultured WW7","ANDENCALAA" },
{ "Uncultured WW8","ANDENYALAA" },
{ "Yersinia enterocolitica","ANDSQYESAALAA" },
{ "Yersinia intermedia","ANDSQYESAALAA" },
{ "Yersinia mollaretii","ANDSQYESAALAA" },
{ "Yersinia bercovieri","ANDSQYESAALAA" },
{ "Yersinia pestis","ANDENYALAA" },
{ "Yersinia frederiksenii","ANDENYALAA" },
{ "Yersinia pseudotuberculosis","ANDENYALAA" },
{ "Mannheimia haemolytica","ANDEQYALAA" },
{ "Mannheimia succiniciproducens","ANDEQYALAA" },
{ "Haemophilus ducreyi","ANDEQYALAA" },
{ "Haemophilus influenzae","ANDEQYALAA" },
{ "Haemophilus somnus","ANDEQYALAA" },
{ "Pasteurella multocida","ANDEQYALAA" },
{ "Actinobacillus actinomycetemcomitans","ANDEQYALAA" },
{ "Actinobacillus pleuropneumoniae","ANDEQYALAA" },
{ "Lawsonia intracellularis","ANNNYDYALAA" },
{ "Desulfovibrio desulfuricans","ANNDYDYAYAA" },
{ "Desulfovibrio vulgaris","ANNYDYALAA" },
{ "Desulfovibrio yellowstonii","ANNELALAA" },
{ "Geobacter sulfurreducens","ADNYDYAVAA" },
{ "Geobacter metallireducens","ADNYDYAVAA" },
{ "Helicobacter pylori 1","VNNTDYAPAYAKAA" },
{ "Helicobacter pylori 2","VNNTDYAPAYAKAA" },
{ "Helicobacter pylori 3","VNNADYAPAYAKAA" },
{ "Campylobacter jejuni","ANNVKFAPAYAKAA" },
{ "Campylobacter lari","ANNVKFAPAYAKAA" },
{ "Campylobacter fetus 2","ANNVKFAPAYAKAA" },
{ "Campylobacter coli","ANNVKFAPAYAKAA" },
{ "Fusobacterium nucleatum 1","GNKDYALAA" },
{ "Fusobacterium nucleatum 2","GNKEYALAA" },
{ "Dehalococcoides ethenogenes","GERELVLAG" },
{ "Mycobacterium leprae","ADSYQRDYALAA" },
{ "Mycobacterium avium","ADSHQRDYALAA" },
{ "Mycobacterium bovis","ADSHQRDYALAA" },
{ "Mycobacterium tuberculosis","ADSHQRDYALAA" },
{ "Mycobacterium marinum","ADSHQRDYALAA" },
{ "Mycobacterium microti","ADSHQRDYALAA" },
{ "Mycobacterium africanum","ADSHQRDYALAA" },
{ "Mycobacterium smegmatis","ADSNQRDYALAA" },
{ "Corynebacterium diphtheriae","AENTQRDYALAA" },
{ "Corynebacterium glutamicum","AEKSQRDYALAA" },
{ "Thermobifida fusca","ANSKRTEFALAA" },
{ "Streptomyces coelicolor","ANTKRDSSQQAFALAA" },
{ "Streptomyces lividans","ANTKRDSSQQAFALAA" },
{ "Tropheryma whipplei","ANLKRTDLSLAA" },
{ "Clavibacter michiganensis","ANNKQSSFVLAA" },
{ "Bifidobacterium longum","AKSNRTEFALAA" },
{ "Bifidobacterium longum","AKSNRTEFALAA" },
{ "Bacillus anthracis","GKQNNLSLAA" },
{ "Bacillus thuringiensis","GKQNNLSLAA" },
{ "Bacillus cereus","GKQNNLSLAA" },
{ "Bacillus megaterium","GKSNNNFALAA" },
{ "Bacillus halodurans","GKENNNFALAA" },
{ "Bacillus clausii","GKENNNFALAA" },
{ "Bacillus subtilis","GKTNSFNQNVALAA" },
{ "Bacillus stearothermophilus","GKQNYALAA" },
{ "Geobacillus kaustophilus","GKQNYALAA" },
{ "Staphylococcus aureus","GKSNNNFAVAA" },
{ "Staphylococcus saprophyticus","GKENNNFAVAA" },
{ "Staphylococcus xylosus","GKENNNFAVAA" },
{ "Staphylococcus epidermidis","DKSNNNFAVAA" },
{ "Oceanobacillus iheyensis","GKETNQPVLAAA" },
{ "Listeria monocytogenes","GKEKQNLAFAA" },
{ "Listeria innocua","GKEKQNLAFAA" },
{ "Listeria welshimeri","GKEKQNLAFAA" },
{ "Listeria seeligeri","GKEKQNLAFAA" },
{ "Listeria grayi 1","GKEKQNLAFAA" },
{ "Listeria grayi 2","GKQNNNLAFAA" },
{ "Listeria ivanovii","GKEKQNLAFAA" },
{ "Lactobacillus gasseri","ANNENSYAVAA" },
{ "Lactobacillus johnsonii","ANNENSYAVAA" },
{ "Lactobacillus sakei","ANNNNSYAVAA" },
{ "Lactobacillus helveticus","ANNKNSYALAA" },
{ "Lactobacillus gallinarum","ANNKNSYALAA" },
{ "Lactobacillus acidophilus","ANNKNSYALAA" },
{ "Lactobacillus plantarum","AKNNNNSYALAA" },
{ "Pediococcus pentosaceus","AKNNNNSYALAA" },
{ "Leuconostoc mesenteroides","AKNENSFAIAA" },
{ "Leuconostoc lactis","AKNENSFAIAA" },
{ "Leuconostoc pseudomesenteroides","AKNENSYAIAA" },
{ "Enterococcus durans","AKNENNSYALAA" },
{ "Oenococcus oeni","AKNNEPSYALAA" },
{ "Enterococcus faecium","AKNENNSYALAA" },
{ "Enterococcus faecalis","AKNENNSFALAA" },
{ "Streptococcus equi","AKNNTTYALAA" },
{ "Streptococcus zooepidemicus","AKNNTTYALAA" },
{ "Streptococcus suis","AKNTNTYALAA" },
{ "Streptococcus uberis","AKNTNSYALAA" },
{ "Streptococcus pyogenes","AKNTNSYALAA" },
{ "Streptococcus agalactiae","AKNTNSYALAA" },
{ "Streptococcus mutans","AKNTNSYAVAA" },
{ "Streptococcus sobrinus","AKNTNSYAVAA" },
{ "Streptococcus gordonii","AKNNTSYALAA" },
{ "Streptococcus pneumoniae","AKNNTSYALAA" },
{ "Streptococcus mitis","AKNNTSYALAA" },
{ "Streptococcus thermophilus","AKNTNSYAVAA" },
{ "Lactococcus raffinolactis","AKNTQTYAVAA" },
{ "Lactococcus plantarum","AKNTQTYALAA" },
{ "Lactococcus garvieae","AKNNTSYALAA" },
{ "Lactococcus lactis","AKNNTQTYAMAA" },
{ "Mycoplasma capricolum","ANKNEETFEMPAFMMNNASAGANFMFA" },
{ "Mesoplasma florum","ANKNEENTNEVPTFMLNAGQANYAFA" },
{ "Spiroplasma kunkelii","ASKKQKEDKIEMPAFMMNNQLAVSMLAA" },
{ "Ureaplasma urealyticum","AENKKSSEVELNPAFMASATNANYAFAY" },
{ "Ureaplasma parvum","AENKKSSEVELNPAFMASATNANYAFAY" },
{ "Mycoplasma pulmonis","GTKKQENDYQDLMISQNLNQNLAFASV" },
{ "Mycoplasma penetrans","AKNNKNEAVEVELNDFEINALSQNANLALYA" },
{ "Mycoplasma genitalium 1","DKENNEVLVEPNLIINQQASVNFAFA" },
{ "Mycoplasma genitalium 2","DKENNEVLVDPNLIINQQASVNFAFA" },
{ "Mycoplasma pneumoniae","DKNNDEVLVDPMLIANQQASINYAFA" },
{ "Thermoanaerobacter tengcongensis","ADRELAYAA" },
{ "Heliobacillus mobilis","AEDNYALAA" },
{ "Desulfitobacterium hafniense","ANDDNYALAA" },
{ "Nitrosococcus oceani","ANDDNYALAA" },
{ "Thiomicrospira crunogena","ANDDNYALAA" },
{ "Stenotrophomonas maltophilia","ANDDNYALAA" },
{ "Carboxydothermus hydrogenoformans","ANENYALAA" },
{ "Ruminococcus albus","GHGYFAKAS" },
{ "Clostridium acetobutylicum","DNENNLALAA" },
{ "Clostridium perfringens","AEDNFALAA" },
{ "Clostridium thermocellum","ANEDNYALAAA" },
{ "Clostridium botulinum","ANDNFALAA" },
{ "Clostridium tetani","ADDNFVLAA" },
{ "Clostridium difficile","ADDNFAIAA" },
{ "Hyphomonas neptunium","ANDNFAEGELLAA" },
{ "Vibrio fischeri","ANDENYALAA" },
{ "Corynebacterium efficiens","AEKTQRDYALAA" },
{ "Streptomyces avermitilus","ANTKSDSQSFALAA" },
{ "Brevibacterium linens","AKSNNRTDFALAA" },
{ "Lactobacillus delbrueckii 1","AKNENNSYALAA" },
{ "Lactobacillus delbrueckii 2","ANENSYAVAA" },
{ "Lactobacillus casei","AKNENSYALAA" },
{ "Lactobacillus brevis","AKNNNNSYALAA" },
{ "Streptomyces thermophilus","AKNTNSYAVAA" },
{ "Bacillusphage G","AKLNITNNELQVA" },
{ "Thermodesulfobacterium commune","ANEYAYALAA" },
{ "Thermomicrobium roseum","GERELALAA" },
{ "Leptospirillum groupII","ANEELALAA" },
{ "Leptospirillum groupIII","ANEELALAA" },
{ "Gloeobacter violaceus","ATNNVVPFARARATVAA" },
{ "Crocosphaera watsonii","ANNIVSFKRVAVAA" },
{ "Thalassiosira pseudonana chloroplast","ANNIMPFMFNVVKTNRSLTTLNFAV" },
{ "Emiliania huxleyi chloroplast","ANNILNFNSKLAIA" },
{ "Cyanidium caldarium chloroplast","ANNIIEISNIRKPALVV" },
{ "Gracilaria tenuistipitata chloroplast","AKNNILTLSRRLIYA" },
{ "Prevotella ruminicola","GNNEYALAA" },
{ "Jannaschia sp. CCS1","ANDNRAPAMALAA" },
{ "Agrobacterium vitis","ANDNNAQGYAVAA" },
{ "Alphaproteobacteria SAR-1","ANDELALAA" },
{ "Gluconobacter oxydans","ANDNSEVLAVAA" },
{ "Sphingomonas elodea","ANDNEALAIAA" },
{ "Ehrlichia ruminantium 1","ANDNFVSANDNNSTANLVAA" },
{ "Ehrlichia ruminantium 2","ANDNFVSANDNNSTANLVAA" },
{ "Ehrlichia canis","ANDNFVFANDNNSSVAGLVAA" },
{ "Anaplasma marginale","ANDDFVAANDNMETAFVAAA" },
{ "Wolbachia sp. 2 (Brugi)","ANDNFAAEGDVAVAA" },
{ "Wolbachia sp. 3 (Culex)","ANDNFAAEDNVALAA" },
{ "Wolbachia sp. 4 (Dros.)","ANDNFAAEEYRVAA" },
{ "Rickettsia rickettsii","ANDNNRSVGRLALAA" },
{ "Tremblaya princeps 1 (Dysmicoccus)",
"APSNRFTIVANDCIDALVRRAVV" },
{ "Azoarcus EbN1","ANDERFAVAA" },
{ "Dechloromonas aromatica","ANDEQFAIAA" },
{ "Dechloromonas agitata","ANDEQFAIAA" },
{ "Thiobacillus denitrificans","AKSKAARRNPACSAGVMELKA" },
{ "Shewanella SAR-2, version 2","ADYGYMAAA" },
{ "Shewanella SAR-1, version 2","ANNDNYALAA" },
{ "Uncultured marineEBAC20E09","ANNDNYALAA" },
{ "Pseudomonas fluorescens 3 (Pf-5)","ANDETYGDYALAA" },
{ "Uncultured remanei","ANDESYALAA" },
{ "Chromohalobacter salexigens","ANDDNYAQGALAA" },
{ "Gammaproteobacteria SAR-1","ANNYNYSLAA" },
{ "Shewanella denitrificans","ANDSNYSLAA" },
{ "Shewanella frigidimarina","ANDSNYSLAA" },
{ "Shewanella baltica","ANDSNYSLAA" },
{ "Photobacterium profundum","ANDENFALAA" },
{ "Blochmannia floridanus","AKNKYNEPVALAA" },
{ "Blochmannia pennsylvanicus","ANNTTYRESVALAA" },
{ "Photorhabdus luminescens","ANDEKYALAA" },
{ "Proteus mirabilis","ANDNQYKALAA" },
{ "Magnetococcus sp.","ANDEHYAPAFAAA" },
{ "Proteobacteria SAR-1, version 1","GENADYALAA" },
{ "Proteobacteria SAR-1, version 2","ANNYNYSLAA" },
{ "Proteobacteria SAR-1, version 3","ADNGYMAAA" },
{ "Desulfovibrio desulfuricans 2 (G20)","ANNDYEYAMAA" },
{ "Uncultured ciona","ANDEFFDARLRA" },
{ "Bacteriovorax marinus","AESNFAPAMAA" },
{ "Bdellovibrio bacteriovorus","GNDYALAA" },
{ "Myxococcus xanthus","ANDNVELALAA" },
{ "Wolinella succinogenes","ALSSHPKRGKRLGLPITSALGA" },
{ "Campylobacter upsaliensis","ANNAKFAPAYAKVA" },
{ "Helicobacter mustelae","ANNKNYAPAYAKVA" },
{ "Helicobacter hepaticus","ANNANYAPAYAKVA" },
{ "Ruminococcus albus","DNDNFAMAA" },
{ "Coprothermobacter proteolyticus","AEPEFALAA" },
{ "Moorella thermoacetica","ADDNLALAA" },
{ "Mycoplasma mycoides","ADKNEENFEMPAFMINNASAGANYMFA" },
{ "Mycoplasma mobile","GKEKQLEVSPLLMSSSQSNLVFA" },
{ "Mycoplasma arthritidis","GNLETSEDKKLDLQFVMNSQTQQNLLFA" },
{ "Paenibacillus larvae","GKQQNNYALAA" },
{ "Bacillus licheniformis","GKSNQNLALAA" },
{ "Actinomyces naeslundii","ADNTRTDFALAA" },
{ "Arthrobacter FB24","AKQTRTDFALAA" },
{ "Leifsonia xyli","ANSKSTVSAKADFALAA" },
{ "Nocardia farcinica","ADSHQREYALAA" },
{ "Propionibacterium acnes 1","AENTRTDFALAA" },
{ "Propionibacterium acnes 2","AENTRTDFALAA" },
{ "Streptomyces collinus","ANTKRDSSSFALAA" },
{ "Streptomyces aureofaciens","ANSKRDSQQFALAA" },
{ "Kineococcus radiotolerans","ADSKRTEFALAA" },
{ "Frankia sp. CcI3","ANKTQPTTPTYALAA" },
{ "Frankia sp. EAN1pec","ATKTQPASSTFALAA" },
{ "Rubrobacter xylanophilus","ANDREMALAA" },
{ "Parachlamydia UWE25","ANNSNKIAKVDFQEGTFARAA" },
{ "Verrucomicrobium spinosum","ANSNELALAA" },
{ "Acidobacterium capsulatum","ANNNLALAA" },
{ "Acidobacterium Ellin6076","ANTQFAYAA" },
{ "Solibacter usitatus","ANTQFAYAA" },
{ "Dictyoglomus thermophilum","ANTNLALAA" },
{ "Mycobacteriophage Bxz1 virion","ATDTDATVTDAEIEAFFAEEAAALV" },
{ "Catera virion","ATDTDATVTDAEIEAFFAEEAAALV" },
{ "Cyanobium gracile","ANNIVRFSRQAAPVAA" },
{ "Anabaena variabilis","ANNIVKFARKDALVAA" },
{ "Nitrosospira multiformis","ANDENYALAA" },
{ "Enterobacter sakazakii","ANDENYALAA" },
{ "Pantoea stewartii","ANDENYALAA" },
{ "Citrobacter rodentium","ANDENYALAA" },
{ "Prochlorococcus marinus","ANNIVSFSRQTAPVAA" },
{ "Azospira oryzae","ANDERFAIAA" },
{ "Uncultured phakopsora","ANDNSYALAA" },
{ "Syntrophus aciditrophicus","ANDYEYALAA" },
{ "Alkaliphilus metalliredigenes","ANDNYSLAAA" },
{ "Caldicellulosiruptor saccharolyticus","ADKAELALAA" } };
n = 0;
st = tag + len;
while (*--st == '*');
for (i = 0; i < NTAG; i++)
{ s = st;
sb = tagdatabase[i].tag;
sd = sb;
while (*++sd);
while (*s-- == *--sd)
{ if (s < tag)
{ if (sd > sb) goto PAR;
if (n >= nt) goto MANY;
copy(tagdatabase[i].name,thit[n]);
n++;
break; }
if (sd > sb) continue;
PAR:
if (n >= nt) goto MANY;
s = copy(tagdatabase[i].name,thit[n]);
copy(" (partial match)",s);
n++;
break; }}
return(n);
MANY:
return(-1); }
void disp_peptide_tag(FILE *f, gene *t, csw *sw)
{ int i,lx,nm,nmh,c1,c2,c3,*s,*se;
char tag[50],thit[21][50];
fprintf(f,"Tag peptide (at %d)\nTag sequence: ",t->tps+1);
se = t->eseq + t->tps;
lx = (t->tpe - t->tps + 1);
if (ltranslate(se+lx,t,sw) == '*')
{ lx += 3;
if (ltranslate(se+lx,t,sw) == '*') lx += 3; }
lx /= 3;
s = se;
for (i = 0; i < lx; i++)
{ if (i > 0) fputc('-',f);
if ((c1 = *s++) >= AMBIG) continue;
if ((c2 = *s++) >= AMBIG) continue;
if ((c3 = *s++) >= AMBIG) continue;
fputc(cbase(c1),f);
fputc(cbase(c2),f);
fputc(cbase(c3),f); }
s = se;
fprintf(f,"\nTag peptide: ");
for (i = 0; i < lx; i++)
{ fprintf(f,"%s",translate(s,sw));
s += 3;
if (i < (lx-1)) fputc('-',f); }
s = se;
fprintf(f,"\nTag peptide: ");
for (i = 0; i < lx; i++)
{ tag[i] = ltranslate(s,t,sw);
fprintf(f,"%c",tag[i]);
s += 3; }
tag[lx] = '\0';
if (sw->energydisp)
{ s = se;
fprintf(f,"\nTag Polarity: ");
for (i = 0; i < lx; i++)
{ fprintf(f,"%c",ptranslate(s,sw));
s += 3; }}
fputc('\n',f);
nmh = identify_tag(tag,lx,thit,21);
if (nmh > 0)
{ if (nmh > 1)
{ fprintf(f,"Match with tmRNA tags from:\n");
i = 0;
for (nm = 0; nm < nmh; nm++)
{ if (++i > 3)
{ fputc('\n',f);
i = 1; }
if (i > 1) fprintf(f,", ");
fprintf(f,"%s",thit[nm]); }
fputc('\n',f); }
else
fprintf(f,"Match with %s tmRNA tag\n",thit[0]); }
else
if (nmh == -1)
fprintf(f,"Match with many tmRNA tags\n");
else
fprintf(f,"Tag not identified\n");
fputc('\n',f); }
void sense_switch(int *seq1, int *seq2, int lseq)
{ int i,b;
int *sseq,*cseq;
sseq = seq1;
cseq = seq2 + lseq;
while (--cseq >= seq2)
{ b = *sseq++;
if (b >= Adenine)
{ if (b <= Thymine)
*cseq = Thymine - b;
else
{ if (b <= NOBASE) *cseq = b;
else *cseq = NOBASE; }}
else *cseq = NOBASE; }}
double nenergy(gene *t, csw *sw)
{ double eref;
if (t->genetype != tRNA) eref = sw->eref[t->genetype];
else
if (sw->mtrna)
{ if (t->dstem == 0) eref = mtRNAtthresh;
else
if (t->tstem == 0) eref = mtRNAdthresh;
else eref = mtRNAdtthresh; }
else eref = sw->eref[tRNA];
return(100.0*t->energy/eref); }
char *position(char *s, gene *t, csw *sw)
{ long start;
start = t->start;
if (sw->linear) if (start <= 0) start--;
if (t->comp)
sprintf(s,"c[%ld,%ld]",start,t->stop);
else
sprintf(s,"[%ld,%ld]",start,t->stop);
return(s); }
void location(char *s, gene *t, csw *sw, char *m)
{ char sp[80];
sprintf(s,"%s %s",m,position(sp,t,sw)); }
void disp_location(gene *t, csw *sw, char *m)
{ char sp[80];
fprintf(sw->f,"%s %s\n",m,position(sp,t,sw)); }
char *name(gene *t, char *si, int proc, csw *sw)
{ int s[5],*ss,*sin,*sm,*s0,*s1,*s2,*s3,nintron;
char *sb,*st;
static char trnatype[2][6] = { "tRNA","mtRNA" };
switch (t->genetype)
{ case CDS:
sprintf(si,"CDS");
break;
case srpRNA:
sprintf(si,"srpRNA");
break;
case tmRNA:
if (t->asst > 0)
sprintf(si,"tmRNA (Permuted)");
else
sprintf(si,"tmRNA");
break;
case tRNA:
ss = (proc?t->seq:t->ps);
sm = ss + t->anticodon - 1;
s0 = sm + 1;
s1 = s0 + 1;
s2 = s1 + 1;
s3 = s2 + 1;
nintron = t->nintron;
if ((proc == 0) && (nintron > 0))
{ sin = ss + t->intron;
if (sm >= sin) sm += nintron;
if (s0 >= sin) s0 += nintron;
if (s1 >= sin) s1 += nintron;
if (s2 >= sin) s2 += nintron;
if (s3 >= sin) s3 += nintron; }
s[0] = *sm;
s[1] = *s0;
s[2] = *s1;
s[3] = *s2;
s[4] = *s3;
st = trnatype[sw->mtrna];
sb = si;
if (t->dstem == 0)
{ sprintf(sb,"D-loop ");
sb += 7; }
if (t->tstem == 0)
{ sprintf(sb,"TV-loop ");
sb += 8; }
if (t->cloop == 8)
sprintf(sb,"%s-?(%s|%s)(%c%c%c%c)",st,
aa(s+1,sw),aa(s+2,sw),
cbase(s[1]),cbase(s[2]),cbase(s[3]),
cbase(s[4]));
else if (t->cloop == 6)
sprintf(sb,"%s-?(%s|%s)(%c%c)",st,
aa(s,sw),aa(s+1,sw),
cbase(s[1]),cbase(s[2]));
else
sprintf(sb,"%s-%s(%c%c%c)",st,
aa(s+1,sw),cbase(s[1]),cbase(s[2]),cbase(s[3]));
break;
default: *si = '\0';
break; }
return(si); }
void disp_intron(FILE *f, gene *t, csw *sw)
{ int i,c,*s,*sb,*se;
char genename[100];
if (t->nintron <= 0) return;
name(t,genename,1,sw);
fprintf(f,"Intron from %s\n",genename);
fprintf(f,"1 . 10 . 20 . 30 . 40 . 50\n");
sb = t->eseq + t->intron;
s = sb;
se = sb + t->nintron;
i = 0;
while (s < se)
{ if ((c = *s++) < Adenine) break;
fputc(cbase(c),f);
if (++i >= 50)
{ fputc('\n',f);
i = 0; }}
if (i > 0) fputc('\n',f);
fputc('\n',f);
fprintf(f,"Intron Length: %d\n",t->nintron);
fprintf(f,"Intron Insertion Position(%d-%d): ",t->intron,t->intron+1);
s = sb - 5;
for (i = 0; i < 5; i++) fputc(cbase(*s++),f);
fprintf(f,"-Intron-");
s = se;
for (i = 0; i < 5; i++) fputc(cbase(*s++),f);
fputc('\n',f);
fputc('\n',f); }
void disp_fasta_seq(FILE *f, gene *t, int ns, int n, int nsp, int c, csw *sw)
{ int i,*s,*se;
char genename[100],genepos[100];
if (t->nintron > 0)
{ s = t->eseq;
se = s + t->nbase + t->nintron; }
else
{ s = t->seq;
se = s + t->nbase; }
name(t,genename,1,sw);
position(genepos,t,sw);
if (nsp > 0)
{ if (ns > 0) fprintf(f,">%d-%d%s%s\n",ns,n,genename,genepos);
else fprintf(f,">%s%s\n",genename,genepos); }
else
{ if (ns > 0) fprintf(f,">%d-%d %s %s\n",ns,n,genename,genepos);
else fprintf(f,">%s %s\n",genename,genepos); }
i = 0;
while (s < se)
{ if (c) fputc(cpbase(*s++),f);
else fputc(cbase(*s++),f);
if (++i >= 50)
{ fputc('\n',f);
i = 0; }}
if (i > 0) fputc('\n',f); }
void disp_seq(FILE *f, gene *t, csw *sw)
{ int i,j,k,varbp,stem,ab,ae,hl,*s,*se,*sl,*sb,*sr;
char genename[100];
static int bplb[2] = { '.','(' };
static int bprb[2] = { '.',')' };
if (t->nintron > 0)
{ s = t->eseq;
se = s + t->nbase + t->nintron; }
else
{ s = t->seq;
se = s + t->nbase; }
if (sw->seqdisp >= 3)
{ if (!sw->batch) fputc('\n',f);
if (sw->seqdisp == 3) disp_fasta_seq(f,t,0,0,0,0,sw);
else disp_fasta_seq(f,t,0,0,0,1,sw); }
else
{ if (!sw->batch)
{ name(t,genename,1,sw);
fprintf(f,"\nPrimary sequence for %s\n",genename); }
if ((sw->seqdisp == 2) && (t->genetype == tRNA))
{ sl = s;
while (sl < se) fputc(cbase(*sl++),f);
fputc('\n',f);
sl = s;
sr = se - t->aatail - 1;
for (i = 0; i < t->astem1; i++,sl++,sr--) fputc(bplb[bp[*sl][*sr]],f);
for (i = 0; i < t->spacer1; i++) fputc(' ',f);
sl += t->spacer1;
sb = sl + t->dstem - 1;
sr = sb + t->dstem + t->dloop;
for (i = 0; i < t->dstem; i++,sl++,sr--) fputc(bplb[bp[*sl][*sr]],f);
for (i = 0; i < t->dloop; i++) fputc('d',f);
sl += t->dloop;
for (i = 0; i < t->dstem; i++,sl++,sb--) fputc(bprb[bp[*sl][*sb]],f);
for (i = 0; i < t->spacer2; i++) fputc(' ',f);
sl += t->spacer2;
sb = sl + t->cstem - 1;
sr = sb + t->cstem + t->cloop + t->nintron;
for (i = 0; i < t->cstem; i++,sl++,sr--) fputc(bplb[bp[*sl][*sr]],f);
hl = t->astem1 + t->spacer1 + 2*t->dstem + t->dloop +
t->spacer2 + t->cstem;
if (t->nintron > 0)
{ j = t->intron - hl;
ab = t->anticodon - hl;
ae = ab + t->cloop - 5;
for (i = 0; i < j; i++)
if (i <= ae)
if (i >= ab) fputc('A',f);
else fputc(' ',f);
else fputc(' ',f);
for (i = 0; i < t->nintron; i++) fputc('i',f);
for (i = j; i < t->cloop; i++)
if (i <= ae)
if (i >= ab) fputc('A',f);
else fputc(' ',f);
else fputc(' ',f); }
else
{ j = t->cloop - 4;
ab = t->anticodon - hl;
ae = t->cloop - ab - j;
for (i = 0; i < ab; i++) fputc(' ',f);
for (i = 0; i < j; i++) fputc('A',f);
for (i = 0; i < ae; i++) fputc(' ',f); }
sl += (t->cloop + t->nintron);
for (i = 0; i < t->cstem; i++,sl++,sb--) fputc(bprb[bp[*sl][*sb]],f);
varbp = find_var_hairpin(t);
if (varbp > 0)
{ j = (varbp >> 10);
k = (varbp >> 5) & 0x1f;
stem = (varbp & 0x1f);
sr = sl + k + stem - 1;
sl += j;
sb = sl + stem - 1;
for (i = 0; i < j; i++) fputc(' ',f);
for (i = 0; i < stem; i++,sl++,sr--) fputc(bplb[bp[*sl][*sr]],f);
for (i = j+stem; i < k; i++,sl++) fputc('v',f);
for (i = 0; i < stem; i++,sl++,sb--) fputc(bprb[bp[*sl][*sb]],f);
for (i = k+stem; i < t->var; i++,sl++) fputc(' ',f); }
else
{ for (i = 0; i < t->var; i++) fputc(' ',f);
sl += t->var; }
sb = sl + t->tstem - 1;
sr = sb + t->tstem + t->tloop;
for (i = 0; i < t->tstem; i++,sl++,sr--) fputc(bplb[bp[*sl][*sr]],f);
for (i = 0; i < t->tloop; i++) fputc('t',f);
sl += t->tloop;
for (i = 0; i < t->tstem; i++,sl++,sb--) fputc(bprb[bp[*sl][*sb]],f);
sb = s + t->astem1 - 1;
for (i = 0; i < t->astem2; i++,sl++,sb--) fputc(bprb[bp[*sl][*sb]],f);
fputc('\n',f); }
else
{ if (!sw->batch)
fprintf(f,"1 . 10 . 20 . 30 . 40 . 50\n");
i = 0;
while (s < se)
{ fputc(cbase(*s++),f);
if (++i >= 50)
{ fputc('\n',f);
i = 0; }}
if (i > 0) fputc('\n',f); }}
if (!sw->batch)
{ fputc('\n',f);
fputc('\n',f); }}
void disp_tmrna_seq(FILE *f, gene *t, csw *sw)
{ int i,*s,*sb,*se;
if (t->nintron <= 0) return;
if (*(t->name) == '\0') fprintf(f,"tmRNA Sequence\n\n");
else fprintf(f,"tmRNA Sequence in %s\n\n",t->name);
fprintf(f,"1 . 10 . 20 . 30 . 40 . 50\n");
sb = t->eseq;
s = sb;
se = sb + t->intron;
i = 0;
while (s < se)
{ fputc(cbase(*s++),f);
if (++i >= 50)
{ fputc('\n',f);
i = 0; }}
se = sb + t->tps;
while (s < se)
{ fputc(cpbase(*s++),f);
if (++i >= 50)
{ fputc('\n',f);
i = 0; }}
se = sb + t->tpe + 1;
while (ltranslate(se,t,sw) == '*') se += 3;
while (s < se)
{ fputc(cbase(*s++),f);
if (++i >= 50)
{ fputc('\n',f);
i = 0; }}
se = sb + t->intron + t->nintron;
while (s < se)
{ fputc(cpbase(*s++),f);
if (++i >= 50)
{ fputc('\n',f);
i = 0; }}
se = sb + t->nbase + t->nintron;
while (s < se)
{ fputc(cbase(*s++),f);
if (++i >= 50)
{ fputc('\n',f);
i = 0; }}
if (i > 0) fputc('\n',f);
fputc('\n',f);
fprintf(f,"Resume consensus sequence (at %d): ",t->tps - 6);
s = t->eseq + t->tps - 7;
for (i = 0; i < 18; i++) fputc(cbase(*s++),f);
fputc('\n',f);
fputc('\n',f);
disp_peptide_tag(f,t,sw); }
void disp_tmrna_perm_seq(FILE *f, gene *t, csw *sw)
{ int i,*s,*sb,*se;
if (t->nintron <= 0) return;
if (*(t->name) == '\0') fprintf(f,"tmRNA Sequence\n\n");
else fprintf(f,"tmRNA Sequence in %s\n\n",t->name);
fprintf(f,"Permuted\n");
fprintf(f,"1 . 10 . 20 . 30 . 40 . 50\n");
sb = t->eseq;
s = sb;
se = sb + 54;
i = 0;
while (s < se)
{ fputc(cpbase(*s++),f);
if (++i >= 50)
{ fputc('\n',f);
i = 0; }}
se = sb + t->intron;
while (s < se)
{ fputc(cbase(*s++),f);
if (++i >= 50)
{ fputc('\n',f);
i = 0; }}
se = sb + t->asst;
while (s < se)
{ fputc(cpbase(*s++),f);
if (++i >= 50)
{ fputc('\n',f);
i = 0; }}
se = sb + t->asst + t->astem1 + t->dloop + t->cstem;
while (s < se)
{ fputc(cbase(*s++),f);
if (++i >= 50)
{ fputc('\n',f);
i = 0; }}
se = sb + t->tps;
while (s < se)
{ fputc(cpbase(*s++),f);
if (++i >= 50)
{ fputc('\n',f);
i = 0; }}
se = sb + t->tpe + 1;
while (ltranslate(se,t,sw) == '*') se += 3;
while (s < se)
{ fputc(cbase(*s++),f);
if (++i >= 50)
{ fputc('\n',f);
i = 0; }}
se = sb + t->tpe + TMPTRAILER - 54;
while (s <= se)
{ fputc(cpbase(*s++),f);
if (++i >= 50)
{ fputc('\n',f);
i = 0; }}
if (i > 0) fputc('\n',f);
fprintf(f,"\nResume consensus sequence (at %d): ",t->tps - 6);
s = t->eseq + t->tps - 7;
for (i = 0; i < 18; i++) fputc(cbase(*s++),f);
fputc('\n',f);
fputc('\n',f);
disp_peptide_tag(f,t,sw); }
void disp_cds(FILE *f, gene *t, csw *sw)
{ int i,ncodon,*s,*se;
char c;
ncodon = t->nbase/3;
if (!t->tps) ncodon--;
fprintf(f,"\n%d codons, start = %c%c%c, stop = ",ncodon,
cbase(t->seq[0]),cbase(t->seq[1]),cbase(t->seq[2]));
s = t->seq + 3;
while ((i = *s++) != TERM) fputc(cbase(i),f);
if (t->tps) fprintf(f," incomplete");
fprintf(f,"\n1 . 10 . 20 . 30 . 40 . 50\n");
s = t->eseq;
se = s;
while (*se != TERM) se++;
if (t->tps) se -= 3;
i = 0;
while (s < se)
{ c = ltranslate(s,t,sw);
fputc(c,f);
if (++i >= 50)
{ fputc('\n',f);
i = 0; }
s += 3; }
if (i > 0) fputc('\n',f);
if (sw->energydisp)
fprintf(f,"Score = %lg\n",t->energy);
fputc('\n',f);
fputc('\n',f); }
int pseudogene(gene *t)
{
if (t->energy < 100.0) return(1);
if (t->genetype == tRNA)
if (t->cloop != 7)
return(1);
return(0);
}
void disp_gene(gene *t, char m[][MATY], csw *sw)
{ double gc;
char stat[80];
switch(t->genetype)
{ case tmRNA:
build_tmrna(t,m,13,27,sw);
xcopy(m,4,3,"tmRNA (tRNA domain)",19);
break;
case tRNA:
build_trna(t,m,13,27,sw);
name(t,stat,1,sw);
xcopy(m,4,3,stat,length(stat));
break; }
location(stat,t,sw,"Sequence");
xcopy(m,4,1,stat,length(stat));
gc = gc_content(t);
sprintf(stat,"%d bases, %%GC = %2.1f",t->nbase,100.0*gc);
xcopy(m,4,2,stat,length(stat));
if (sw->reportpseudogenes)
if (pseudogene(t))
xcopy(m,4,4,"Possible Pseudogene",19);
if (sw->energydisp)
{ sprintf(stat,"Score = %g\n",t->energy);
xcopy(m,4,0,stat,length(stat)); }}
void disp_batch_trna(FILE *f, gene *t, csw *sw)
{ int ls,ps,*s,anticodon;
char pos[50],species[50];
static char type[2][6] = { "tRNA","mtRNA" };
static char asterisk[2] = { ' ','*'};
anticodon = 1 + t->anticodon;
if (t->nintron > 0)
if (t->intron <= t->anticodon)
anticodon += t->nintron;
s = t->seq + t->anticodon;
ps = sw->reportpseudogenes?(pseudogene(t)?1:0):0;
switch(t->cloop)
{ case 6:
case 8:
sprintf(species,"%s-???%c",type[sw->mtrna],asterisk[ps]);
break;
case 7:
default:
sprintf(species,"%s-%s%c",type[sw->mtrna],aa(s,sw),asterisk[ps]);
break; }
position(pos,t,sw);
ls = length(species);
if (ls <= 10) fprintf(f,"%-10s%28s",species,pos);
else if (ls <= 17) fprintf(f,"%-17s%21s",species,pos);
else fprintf(f,"%-25s%13s",species,pos);
if (sw->energydisp)
{ fprintf(f,"\t%5.1f",t->energy); }
fprintf(f,"\t%-4d",anticodon);
switch(t->cloop)
{ case 6:
fprintf(f,"\t(%c%c) ",cbase(*s),cbase(s[1]));
break;
case 8:
fprintf(f,"\t(%c%c%c%c) ",
cbase(*s),cbase(s[1]),cbase(s[2]),cbase(s[3]));
break;
case 7:
default:
fprintf(f,"\t(%c%c%c)",cbase(*s),cbase(s[1]),cbase(s[2]));
break; }
if (t->nintron > 0)
fprintf(f,"i(%d,%d)",t->intron+1,t->nintron);
fputc('\n',f);
if (sw->seqdisp) disp_seq(f,t,sw); }
void disp_batch_tmrna(FILE *f, gene *t, csw *sw)
{ int ps,tpe,*sb,*se;
char pos[50];
static char permask[2][2][3] =
{ {" ","p "},{"* ","p*"} };
ps = (t->energy < 100.0)?1:0;
position(pos,t,sw);
fprintf(f,"tmRNA%2s%31s",permask[(t->asst == 0)?0:1][ps],pos);
if (sw->energydisp)
{ fprintf(f,"\t%5.1f\t",t->energy); }
tpe = t->tpe;
sb = t->eseq + t->tps;
se = t->eseq + tpe + 1;
while (ltranslate(se,t,sw) == '*')
{ se += 3;
tpe += 3; }
fprintf(f,"\t%d,%d\t",t->tps+1,tpe+1);
while (sb < se)
{ fputc(ltranslate(sb,t,sw),f);
sb += 3; }
fputc('\n',f);
if (sw->seqdisp) disp_seq(f,t,sw); }
void disp_batch_srprna(FILE *f, gene *t, csw *sw)
{ int ps,tpe,*sb,*se;
char pos[50];
static char asterisk[2] = { ' ','*'};
ps = (t->energy < 100.0)?1:0;
position(pos,t,sw);
fprintf(f,"srpRNA%c %25s",asterisk[ps],pos);
if (sw->energydisp)
{ fprintf(f,"\t%5.1f",t->energy); }
fputc('\n',f);
if (sw->seqdisp) disp_seq(f,t,sw); }
void disp_batch_cds(FILE *f, gene *t, csw *sw)
{ int ps,tpe,*sb,*se;
char pos[50];
static char asterisk[2] = { ' ','*'};
ps = (t->energy < 100.0)?1:0;
position(pos,t,sw);
fprintf(f,"CDS%c %25s",asterisk[ps],pos);
if (sw->energydisp)
{ fprintf(f,"\t%5.1f",t->energy); }
fputc('\n',f);
if (sw->seqdisp) disp_seq(f,t,sw); }
double vloop_stability(int *sb, int var, int *varbp)
{ int e,stem,vstem,loop,*sn,*sen,*pos1,*pos2,*se,*sc,*sd,*sf,*s;
unsigned int c,cn,m;
static unsigned int A[6] = { 0,0,0x100,0x400,0,0 };
static unsigned int C[6] = { 0,0,0x400,0,0,0 };
static unsigned int G[6] = { 0x100,0x400,0,0x200,0,0 };
static unsigned int T[6] = { 0x400,0,0x200,0,0,0 };
static unsigned int te[6] = { 0,0,0,0,0,0 };
e = 0;
sc = sb + 3;
se = sb + var - 2;
sf = se - 2;
te[0] = A[*se];
te[1] = C[*se];
te[2] = G[*se];
te[3] = T[*se];
while (--se > sf)
{ te[0] = (te[0] >> 4) | A[*se];
te[1] = (te[1] >> 4) | C[*se];
te[2] = (te[2] >> 4) | G[*se];
te[3] = (te[3] >> 4) | T[*se]; }
while (se >= sc)
{ te[0] = ((te[0] >> 4) | A[*se]);
te[1] = ((te[1] >> 4) | C[*se]);
te[2] = ((te[2] >> 4) | G[*se]);
te[3] = ((te[3] >> 4) | T[*se]);
s = se - 5;
sd = se - 7;
m = te[*s];
while (--s > sd) m = (m >> 4) + te[*s];
while (s >= sb)
{ m = (m >> 4) + te[*s];
c = m & 0xf;
if (c >= 9)
{ stem = 3;
loop = (int)(se - s) - 3;
sen = se;
sn = s + 2;
while (loop >= 6)
{ if ((cn = vbp[sen[-1]][sn[1]]) <= 0) break;
c += cn;
stem++;
loop -= 2;
sen--;
sn++; }
if (c > e)
{ e = c;
pos1 = s;
pos2 = sen;
vstem = stem; }}
s--; }
se--; }
if (e > 0)
{ *varbp = (((int)(pos1-sb))<<10) + (((int)(pos2-sb))<<5) + vstem;
return((double)(3*(vstem - 4))); }
else
{ *varbp = 0;
return(-12.0); }}
double find_tag_upstream_hairpin(int *se)
{ int *sb,*sd,*sf,*sh,*s;
unsigned int c,m,mx;
static unsigned int A[6] = { 0,0,0,0x10000,0,0 };
static unsigned int C[6] = { 0,0,0x10000,0,0,0 };
static unsigned int G[6] = { 0,0x10000,0,0x10000,0,0 };
static unsigned int T[6] = { 0x10000,0,0x10000,0,0,0 };
static unsigned int t[6] = { 0,0,0,0,0,0 };
mx = 0;
sf = se - 4;
sb = se - 20;
t[0] = A[*se];
t[1] = C[*se];
t[2] = G[*se];
t[3] = T[*se];
while (--se > sf)
{ t[0] = (t[0] >> 4) | A[*se];
t[1] = (t[1] >> 4) | C[*se];
t[2] = (t[2] >> 4) | G[*se];
t[3] = (t[3] >> 4) | T[*se]; }
sh = se - 4;
sd = se - 30;
while (se > sb)
{ t[0] = ((t[0] >> 4) | A[*se]);
t[1] = ((t[1] >> 4) | C[*se]);
t[2] = ((t[2] >> 4) | G[*se]);
t[3] = ((t[3] >> 4) | T[*se]);
s = sh;
m = t[*s];
while (--s > sd)
{ m = (m >> 4) + t[*s];
c = m & 0xf;
if (c > mx) mx = c;
if (mx == 5) goto FND; }
sd--;
sh--;
se--; }
return(0.0);
FND:
return(15.0); }
double find_taghairpin(int *seq)
{ int i,*s,*sb,*se,*sf;
unsigned int c,m,mx;
static unsigned int A[6] = { 0,0,0,1,0,0 };
static unsigned int C[6] = { 0,0,1,0,0,0 };
static unsigned int G[6] = { 0,1,0,1,0,0 };
static unsigned int T[6] = { 1,0,1,0,0,0 };
static unsigned int t[6] = { 0,0,0,0,0,0 };
mx = 0;
sb = seq - 20;
se = seq - 13;
sf = seq - 4;
t[0] = A[*sb];
t[1] = C[*sb];
t[2] = G[*sb];
t[3] = T[*sb];
while (++sb < se)
{ t[0] = (t[0] << 4) | A[*sb];
t[1] = (t[1] << 4) | C[*sb];
t[2] = (t[2] << 4) | G[*sb];
t[3] = (t[3] << 4) | T[*sb]; }
while (sb < sf)
{ t[0] = ((t[0] << 4) | A[*sb]) & 0xffffffff;
t[1] = ((t[1] << 4) | C[*sb]) & 0xffffffff;
t[2] = ((t[2] << 4) | G[*sb]) & 0xffffffff;
t[3] = ((t[3] << 4) | T[*sb]) & 0xffffffff;
sb++;
s = seq + 20;
se = seq + 2;
m = t[*s--];
while (s > se)
{ m = (m >> 4) + t[*s--];
c = m & 0xf;
if (c > mx) mx = c; }
i = 7 - (int)mx;
while (i-- > 0)
{ m = m >> 4;
c = m & 0xf;
if (c > mx) mx = c; }}
return((double)(mx << 1)); }
double stem_energy(int *s1, int *s2, int stem)
{ int *se;
double energy;
static double bem[6][6] =
{ { -1.072,-0.214,-1.072, ATBOND, 0.000, 0.000 },
{ -0.214,-1.072, 3.000,-1.072, 0.000, 0.000 },
{ -1.072, 3.000,-1.072, 1.286, 0.000, 0.000 },
{ ATBOND,-1.072, 1.286,-0.214, 0.000, 0.000 },
{ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000 },
{ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000 } };
se = s1 + stem;
energy = bem[*s1++][*--s2];
while (s1 < se)
energy += bem[*s1++][*--s2];
return(energy); }
double astem_energy(int *s1, int *s2, int stem)
{ int *se;
double energy;
static double abem[6][6] =
{ { -2.144,-0.428,-2.144, ATBOND, 0.000, 0.000 },
{ -0.428,-2.144, 3.000,-2.144, 0.000, 0.000 },
{ -2.144, 3.000,-2.144, 1.286, 0.000, 0.000 },
{ ATBOND,-2.144, 1.286,-0.428, 0.000, 0.000 },
{ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000 },
{ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000 } };
se = s1 + stem;
energy = abem[*s1++][*--s2];
while (s1 < se)
energy += abem[*s1++][*--s2];
return(energy); }
void trna_score(FILE *f, gene *t)
{ int *s,*tpos,tarm,varbp;
double ea,eta,evls;
static double bem[6][6] =
{ { -2.144,-0.428,-2.144, ATBOND, 0.000, 0.000 },
{ -0.428,-2.144, 3.000,-2.144, 0.000, 0.000 },
{ -2.144, 3.000,-2.144, 1.286, 0.000, 0.000 },
{ ATBOND,-2.144, 1.286,-0.428, 0.000, 0.000 },
{ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000 },
{ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000 } };
static double A[6] = { 1.0,0.0,0.0,0.0,0.0,0.0 };
static double C[6] = { 0.0,1.0,0.0,0.0,0.0,0.0 };
static double G[6] = { 0.0,0.0,1.0,0.0,0.0,0.0 };
static double T[6] = { 0.0,0.0,0.0,1.0,0.0,0.0 };
if (t->genetype != tRNA) return;
tarm = 2*t->tstem + t->tloop;
tpos = t->seq + t->astem1 + t->spacer1 + t->dloop + 2*t->dstem + 1 +
2*t->cstem + t->cloop + t->var;
s = tpos + t->tstem - 1;
eta = 6.0*(G[s[0]] + T[s[1]] + T[s[2]] + C[s[3]]) + 3.0*A[s[1]];
s += t->tloop - 3;
eta += 2.0*(G[*s] + A[s[1]] + T[s[3]] + C[s[4]] + C[s[5]]);
eta += astem_energy(tpos,tpos+tarm,t->tstem);
eta += bem[tpos[t->tstem]][tpos[t->tstem + 4]];
eta -= 3.0*(double)(5 - t->tstem);
if (t->tloop > 7) eta -= 3.0*(double)(t->tloop - 7);
else eta -= 3.0*(double)(7 - t->tloop);
s = t->seq;
if (t->astem1 > 7) s++;
ea = astem_energy(s,tpos+tarm+7,7);
if (t->var > 17) evls = vloop_stability(tpos-t->var,t->var,&varbp);
else evls = 0.0;
fprintf(f,"\n");
fprintf(f," T-arm score: %g\n",eta);
fprintf(f," A-stem score: %g\n",ea);
fprintf(f," V-loop stability: %g\n",evls);
fprintf(f,"\n"); }
void tmrna_score(FILE *f, gene *t, csw *sw)
{ int r,j,te,*s,*sb,*se,*tpos,tarm;
double e,er,et,eal,esp,ed,ec,ea,egga,etcca,egg,eta,edgg;
double ehairpin,euhairpin;
static int gtemplate[6] = { 0x00,0x00,0x11,0x00,0x00,0x00 };
static double tagend_score[4] = { 36.0, 66.0, 62.0, 72.0 };
static int nps[126] =
{ 0,0,0,0,
0,0,0,0,
0,0,0,0,
1,1,1,1,
0,0,0,0,
1,1,1,1,
0,0,0,0,
1,1,1,1,
0,0,0,0,
1,1,1,1,
1,1,1,1,
1,1,1,1,
2,1,2,1,
0,0,0,0,
2,1,1,1,
1,1,1,1,
0,0,0,0,
0,0,0,0,
0,0,0,0,
0,0,0,0,
0,0,0,0,
0,0,0,0 };
static double bem[6][6] =
{ { -2.144,-0.428,-2.144, ATBOND, 0.000, 0.000 },
{ -0.428,-2.144, 3.000,-2.144, 0.000, 0.000 },
{ -2.144, 3.000,-2.144, 1.286, 0.000, 0.000 },
{ ATBOND,-2.144, 1.286,-0.428, 0.000, 0.000 },
{ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000 },
{ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000 } };
static double A[6] = { 1.0,0.0,0.0,0.0,0.0,0.0 };
static double C[6] = { 0.0,1.0,0.0,0.0,0.0,0.0 };
static double G[6] = { 0.0,0.0,1.0,0.0,0.0,0.0 };
static double K[6] = { 0.0,0.0,1.0,1.0,0.0,0.0 };
static double R[6] = { 1.0,0.0,1.0,0.0,0.0,0.0 };
static double T[6] = { 0.0,0.0,0.0,1.0,0.0,0.0 };
static double Y[6] = { 0.0,1.0,0.0,1.0,0.0,0.0 };
static double nA[6] = { 0,1.0,1.0,1.0,1.0,1.0 };
static double nV[6] = { 0,0,0,1.0,1.0,1.0 };
static double nM[6] = { 0,0,1.0,1.0,1.0,1.0 };
if (t->genetype != tmRNA) return;
tarm = 2*t->tstem + t->tloop;
s = t->eseq + t->tps - 7;
er = A[s[1]]+2.0*T[s[2]]+C[s[2]]+3.0*A[s[3]]+R[s[4]]+Y[s[6]]+
3.0*G[s[7]]+C[s[8]];
if (sw->tmstrict) er -= (nV[s[10]] + nV[s[11]] + nM[s[14]] + nA[s[17]]);
er *= 4.0;
s = t->eseq + t->tpe - 8;
te = ((nps[(s[0]<<4) + (s[1]<<2) + s[2]] & 1) << 1)
| (nps[(s[3]<<4) + (s[4]<<2) + s[5]] & 1);
et = tagend_score[te];
if (sw->tmstrict)
{ eal = 0.0;
j = -3;
while (j < 6)
{ te = s[j++];
te = (te << 2) | s[j++];
if (te == 9) eal = (double)(11 + 2*((j + 1)/3));
j++; }
ehairpin = find_taghairpin(s + 8);
euhairpin = find_tag_upstream_hairpin(t->eseq + t->tps - 10); }
else
{ eal = 15.0;
ehairpin = 16.0;
euhairpin = 15.0; }
tpos = t->eseq;
if (t->asst > 0)
{ tpos += t->cstem + t->var + 54;
ed = 0.0; }
else
{ tpos += t->astem1 + t->dloop + 2*t->cstem + t->nintron + t->var;
ed = 0.001*(double)(t->tps - (long)(tpos - t->eseq)); }
s = tpos + t->tstem - 10;
e = K[s[0]] + G[s[1]] + A[s[2]];
egga = K[s[1]] + G[s[2]] + A[s[3]];
if (e > egga) egga = e;
egga *= 6.0;
if (egga < 18.0) egga = 0.0;
s = tpos + tarm + 4;
etcca = 10.0*(T[s[0]] + C[s[1]] + C[s[2]] + A[s[3]]);
s = t->eseq + t->asst;
egg = 7.0*(G[s[1]] + G[s[2]]);
edgg = 0.0;
s = t->eseq + t->asst + t->astem1;
sb = s + 3;
se = s + 7;
r = gtemplate[*sb++];
while (sb < se)
{ r = (r >> 4) + gtemplate[*sb++];
if ((r & 3) == 2)
{ edgg = 14.0;
break; }}
s = tpos + t->tstem - 1;
if (sw->tmstrict && (t->asst == 0))
eta = 6.0*(G[s[0]] + T[s[1]] + T[s[2]] + C[s[3]]) + 3.0*A[s[1]];
else
eta = 6.0*(G[s[0]] + (G[s[1]] + T[s[1]]) +
(G[s[2]] + T[s[2]]) + C[s[3]]) + 3.0*A[s[1]];
s += t->tloop - 3;
eta += 2.0*(G[*s] + A[s[1]] + T[s[3]] + C[s[4]] + C[s[5]]);
eta += astem_energy(tpos,tpos+tarm,t->tstem);
eta += bem[tpos[t->tstem]][tpos[t->tstem + 4]];
eta -= 3.0*(double)(5 - t->tstem);
if (t->tloop > 7) eta -= 3.0*(double)(t->tloop - 7);
else eta -= 3.0*(double)(7 - t->tloop);
eta *= 1.59;
s = t->eseq + t->asst + t->astem1 + t->dloop;
ec = stem_energy(s,tpos-t->var,t->cstem);
s = t->eseq + t->asst;
ea = astem_energy(s,tpos+tarm+t->astem1,t->astem1);
esp = ((t->tpe - t->tps) < 24)?-15.0:0.0;
e = er + et + ed + eal + esp + egga + egg + etcca + eta + ec + ea +
edgg + ehairpin + euhairpin;
fprintf(f,"\n");
fprintf(f," Resume sequence score: %g\n",er);
fprintf(f,"Resume-Tarm distance score: %g\n",ed);
fprintf(f," Tag peptide score: %g\n",et);
fprintf(f," Tag end alanine score: %g\n",eal);
fprintf(f," Short tag penalty: %g\n",esp);
fprintf(f," Tag hairpin score: %g\n",ehairpin);
fprintf(f,"Tag upstream hairpin score: %g\n",euhairpin);
fprintf(f," V-loop GGA score: %g\n",egga);
fprintf(f," A-stem GG score: %g\n",egg);
fprintf(f," A-stem TCCA score: %g\n",etcca);
fprintf(f," D-loop GG score: %g\n",edgg);
fprintf(f," T-arm score: %g\n",eta);
fprintf(f," C-stem score: %g\n",ec);
fprintf(f," A-stem score: %g\n",ea);
fprintf(f," C-stem + A-stem score: %g\n",ea + ec);
fprintf(f," Total score: %g\n",e);
fprintf(f," Normalised score: %g\n",nenergy(t,sw));
fprintf(f,"\n"); }
int find_tstems(int *s, int ls, trna_loop hit[], int nh, csw *sw)
{ int i,r,c,tstem,tloop,ithresh1;
int *s1,*s2,*se,*ss,*si,*sb,*sc,*sf,*sl,*sx,*template;
double ec,energy,penalty,thresh2;
static double bem[6][6] =
{ { -2.144,-0.428,-2.144, ATBOND, 0.000, 0.000 },
{ -0.428,-2.144, 3.000,-2.144, 0.000, 0.000 },
{ -2.144, 3.000,-2.144, 1.286, 0.000, 0.000 },
{ ATBOND,-2.144, 1.286,-0.428, 0.000, 0.000 },
{ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000 },
{ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000 } };
static double A[6] = { 2.0,0.0,0.0,0.0,0.0,0.0 };
static double C[6] = { 0.0,2.0,0.0,0.0,0.0,0.0 };
static double G[6] = { 0.0,0.0,2.0,0.0,0.0,0.0 };
static double T[6] = { 0.0,0.0,0.0,2.0,0.0,0.0 };
static int template_trna[6] =
{ 0x0100, 0x0002, 0x2000, 0x0220, 0x0000, 0x0000 };
static int template_tmrna[6] =
{ 0x0100, 0x0002, 0x2220, 0x0220, 0x0000, 0x0000 };
i = 0;
template = (sw->tmrna)?template_tmrna:template_trna;
ithresh1 = (int)sw->ttscanthresh;
thresh2 = sw->ttarmthresh;
ss = s + sw->loffset;
si = ss + 4 - 1;
sl = s + ls - sw->roffset + 5 + 3;
r = template[*si++];
r = (r >> 4) + template[*si++];
r = (r >> 4) + template[*si++];
while (si < sl)
{ r = (r >> 4) + template[*si++];
if ((c = (r & 0xF)) < ithresh1) continue;
sb = si - 7;
sf = sb + 13;
ec = (double)(3*c);
for (tstem = 4; tstem <= 5; tstem++)
{ if (sb >= (sl-8)) goto NX;
sc = sf;
sx = si - 2;
for (tloop = 5; tloop <= 9; tloop++)
{ if (tloop > 7)
penalty = 3.0*(double)(tloop - tstem - 2);
else
penalty = 3.0*(double)(12 - tloop - tstem);
s1 = sb;
s2 = sc;
se = s1 + tstem;
energy = ec + bem[*se][se[4]] + bem[*s1++][*--s2] - penalty;
while (s1 < se) energy += bem[*s1++][*--s2];
energy += G[*sx] + A[sx[1]] + T[sx[3]] + C[sx[4]] + C[sx[5]];
if (energy >= thresh2)
{ if (i >= nh)
{ fprintf(stderr,"Too many tstem hits\n");
goto FN; }
hit[i].pos = sb;
hit[i].loop = tloop;
hit[i].stem = tstem;
hit[i].energy = energy;
i++; }
sx++;
sc++; }
NX:
if (--sb < ss) break;
sf++; }}
FN:
return(i); }
int find_astem5(int *si, int *sl, int *astem3, int n3,
trna_loop hit[], int nh, csw *sw)
{ int i,k;
int *s1,*s2,*se;
unsigned int r,tascanthresh;
double tastemthresh,energy;
static unsigned int template[6] = { 0,0,0,0,0,0 };
static unsigned int A[6] = { 0,0,0,2,0,0 };
static unsigned int C[6] = { 0,0,2,0,0,0 };
static unsigned int G[6] = { 0,2,0,1,0,0 };
static unsigned int T[6] = { 2,0,1,0,0,0 };
static double abem[6][6] =
{ { -2.144,-0.428,-2.144, ATBOND, 0.000, 0.000 },
{ -0.428,-2.144, 3.000,-2.144, 0.000, 0.000 },
{ -2.144, 3.000,-2.144, 1.286, 0.000, 0.000 },
{ ATBOND,-2.144, 1.286,-0.428, 0.000, 0.000 },
{ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000 },
{ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000 } };
tascanthresh = (unsigned int)sw->tascanthresh;
tastemthresh = sw->tastemthresh;
i = 0;
sl += n3;
se = astem3 + n3 - 1;
template[0] = A[*se];
template[1] = C[*se];
template[2] = G[*se];
template[3] = T[*se];
while (--se >= astem3)
{ template[0] = (template[0] << 4) + A[*se];
template[1] = (template[1] << 4) + C[*se];
template[2] = (template[2] << 4) + G[*se];
template[3] = (template[3] << 4) + T[*se]; }
r = template[*si++];
k = 1;
while (++k < n3) r = (r >> 4) + template[*si++];
while (si < sl)
{ r = (r >> 4) + template[*si++];
if ((r & 15) >= tascanthresh)
{ s1 = astem3;
s2 = si;
se = s1 + n3;
energy = abem[*s1++][*--s2];
while (s1 < se)
energy += abem[*s1++][*--s2];
if (energy >= tastemthresh)
{ if (i >= nh)
{ fprintf(stderr,"Too many astem5 hits\n");
goto FN; }
hit[i].pos = si - n3;
hit[i].energy = energy;
i++; }}}
FN:
return(i); }
/*
Resume consensus sequence is: WAUARNYGCNAANNANNA
Williams, K. P., Martindale, K. A. & Bartel, D. P. (1999)
EMBO J. 18, 5423-5433
A more general consensus sequence is NATARNYGCNRVNNMNNH
aragorn strict search uses NATARNYGCNRVNNMNNA
aragorn relaxed search uses NATARNYGC
R = A or G
Y = C or T
W = A or T
V = A or C or G
M = A or C
H = A or C or T
K = G or T
*/
int find_resume_seq(int *s, int ls, trna_loop hit[], int nh, csw *sw)
{ int e,i,j,k,a,aa[3],*si,*sb,*sf,*st,*sl;
double al;
unsigned int r,c,thresh;
static int nps[105] =
{ 0,0,0,0, 0,0,0,0,
0,0,0,0, 1,1,1,1,
0,0,0,0, 1,1,1,1,
0,0,0,0, 1,1,1,1,
0,0,0,0, 1,1,1,1,
1,1,1,1, 1,1,1,1,
0,1,0,1, 0,0,0,0,
0,1,1,1, 1,1,1,1,
0,0,0,0, 0,0,0,0,
0,0,0,0, 0,0,0,0,
0,0,0,0, 0,0,0,0,
0,0,0,0, 0,0,0,0,
0,0,0,0, 0,0,0,0,0 };
static double score[4] = { 36.0, 66.0, 62.0, 72.0 };
static unsigned int template[6] =
{ 0x10310000, 0x01000101, 0x00010030,
0x02000100, 0x00000000, 0x00000000 };
static int A[6] = { 0,1,1,1,1,1 };
static int V[6] = { 0,0,0,1,1,1 };
static int M[6] = { 0,0,1,1,1,1 };
thresh = (unsigned int)sw->tmrthresh;
i = 0;
sl = s + ls;
r = template[*s++];
r = (r >> 4) + template[*s++];
r = (r >> 4) + template[*s++];
r = (r >> 4) + template[*s++];
r = (r >> 4) + template[*s++];
r = (r >> 4) + template[*s++];
r = (r >> 4) + template[*s++];
if (sw->tmstrict)
while (s < sl)
{ r = (r >> 4) + template[*s++];
if ((c = (r & 0xF)) < thresh) continue;
c -= (V[s[1]] + V[s[2]] + M[s[5]] + A[s[8]]);
if (c < thresh) continue;
if (i >= nh) goto FL;
st = s - 2;
si = st;
sb = st + MINTAGDIST + 2;
sf = st + MAXTAGDIST;
while (si < sf)
{ if (*si++ != Thymine)
si++;
else
if (*si == Adenine)
{ if (!(*++si & 5)) goto ST1; }
else
if (*si == Guanine)
{ if (*++si == Adenine) goto ST1; }
else si++;
si++; }
continue;
ST1:
if (si < sb) continue;
al = 0.0;
k = 0;
j = -11;
while (j < -2)
{ a = si[j++];
a = (a << 2) | si[j++];
if (a == 9) al = (double)(11 + 2*((j + 9)/3));
a = (a << 2) | si[j++];
aa[k++] = a; }
hit[i].pos = st;
hit[i].stem = (int)(si - st);
e = (nps[aa[1]] << 1) | (nps[aa[2]]);
hit[i].energy = (double)(c << 2) + score[e] + al +
find_taghairpin(si) +
find_tag_upstream_hairpin(st-10);
i++; }
else
while (s < sl)
{ r = (r >> 4) + template[*s++];
if ((c = (r & 0xF)) < thresh) continue;
if (i >= nh) goto FL;
st = s - 2;
si = st + MINTAGDIST;
sf = st + MAXTAGDIST;
while (si < sf)
{ if (*si++ != Thymine)
si++;
else
if (*si == Adenine)
{ if (!(*++si & 5)) goto ST2; }
else
if (*si == Guanine)
{ if (*++si == Adenine) goto ST2; }
else si++;
si++; }
continue;
ST2:
hit[i].pos = st;
hit[i].stem = (int)(si - st);
e = (nps[(si[-8] << 4) | (si[-7] << 2) | si[-6]] << 1) |
(nps[(si[-5] << 4) | (si[-4] << 2) | si[-3]]);
hit[i].energy = 46.0 + (double)(c << 2) + score[e];
i++; }
FN:
return(i);
FL:
fprintf(stderr,"Too many resume sequence hits\n");
goto FN; }
int *base_copy3(int *from, int *to, int n)
{ while (n-- > 0) *to++ = *from++;
*to = TERM;
return(to); }
void remove_intron(int *s1, int *s2, int nbase, int intron, int nintron)
{ int *s1e;
s1e = s1 + intron;
nbase -= intron;
while (s1 < s1e) *s2++ = *s1++;
s1 += nintron;
s1e = s1 + nbase;
while (s1 < s1e) *s2++ = *s1++;
*s2 = TERM; }
gene *nearest_trna_gene(data_set *d, int nt, gene *t, csw *sw)
{ int n,i,comp,mtrna,mtcompov,maxintronlen,ilength;
long a,b,c,e,score,thresh,psmax;
static long proximity = 7*MINCTRNALEN/10;
double energy;
psmax = d->psmax;
comp = t->comp;
mtrna = sw->mtrna;
mtcompov = sw->mtcompov;
maxintronlen = sw->maxintronlen;
n = -1;
energy = INACTIVE;
a = t->start;
b = t->stop;
thresh = b-a;
if (b < a)
{ b += psmax;
thresh += psmax;
for (i = 0; i < nt; i++)
{ c = ts[i].start;
e = ts[i].stop;
if (e < c)
{ e += psmax;
if (a > e) goto NXTW;
if (b < c) goto NXTW;
if (ts[i].genetype != tRNA) continue;
if (ts[i].comp != comp)
{ if (!mtrna) continue;
if (mtcompov) continue; }
if (maxintronlen > 0)
{ ilength = e - c;
if ((2*thresh) > (5*ilength)) continue;
if ((2*ilength) > (5*thresh)) continue; }
score = (a >= c)?((b >= e)?e-a:thresh):((b >= e)?thresh:b-c);
if (score >= proximity)
if (ts[i].energy < energy)
{ n = i;
energy = ts[i].energy; }
NXTW:
c -= psmax;
e -= psmax; }
if (a > e) continue;
if (b < c) continue;
if (ts[i].genetype != tRNA) continue;
if (ts[i].comp != comp)
{ if (!mtrna) continue;
if (mtcompov) continue; }
if (maxintronlen > 0)
{ ilength = e - c;
if ((2*thresh) > (5*ilength)) continue;
if ((2*ilength) > (5*thresh)) continue; }
score = (a >= c)?((b >= e)?e-a:thresh):((b >= e)?thresh:b-c);
if (score >= proximity)
if (ts[i].energy < energy)
{ n = i;
energy = ts[i].energy; } }
a -= psmax;
b -= psmax; }
for (i = 0; i < nt; i++)
{ c = ts[i].start;
e = ts[i].stop;
if (e < c)
{ e += psmax;
if (a > e) goto NXTN;
if (b < c) goto NXTN;
if (ts[i].genetype != tRNA) continue;
if (ts[i].comp != comp)
{ if (!mtrna) continue;
if (mtcompov) continue; }
if (maxintronlen > 0)
{ ilength = e - c;
if ((2*thresh) > (5*ilength)) continue;
if ((2*ilength) > (5*thresh)) continue; }
score = (a >= c)?((b >= e)?e-a:thresh):((b >= e)?thresh:b-c);
if (score >= proximity)
if (ts[i].energy < energy)
{ n = i;
energy = ts[i].energy; }
NXTN:
c -= psmax;
e -= psmax; }
if (a > e) continue;
if (b < c) continue;
if (ts[i].genetype != tRNA) continue;
if (ts[i].comp != comp)
{ if (!mtrna) continue;
if (mtcompov) continue; }
if (maxintronlen > 0)
{ ilength = e - c;
if ((2*thresh) > (5*ilength)) continue;
if ((2*ilength) > (5*thresh)) continue; }
score = (a >= c)?((b >= e)?e-a:thresh):((b >= e)?thresh:b-c);
if (score >= proximity)
if (ts[i].energy < energy)
{ n = i;
energy = ts[i].energy; } }
if (n >= 0) return(ts + n);
return(NULL); }
gene *nearest_tmrna_gene(data_set *d, int nt, gene *t)
{ int n,i,comp;
long a,b,c,e,score,smax,thresh,psmax;
psmax = d->psmax;
comp = t->comp;
smax = -1;
n = -1;
a = t->start;
b = t->stop;
thresh = b-a;
if (b < a)
{ b += psmax;
thresh += psmax;
for (i = 0; i < nt; i++)
{ c = ts[i].start;
e = ts[i].stop;
if (e < c)
{ e += psmax;
if (a > e) goto NXTW;
if (b < c) goto NXTW;
if (ts[i].genetype != tmRNA) continue;
if (ts[i].comp != comp) continue;
score = (a >= c)?((b >= e)?e-a:thresh):((b >= e)?thresh:b-c);
if (score >= smax)
if (score > smax)
{ n = i;
smax = score; }
else
if (ts[i].energy < ts[n].energy)
n = i;
NXTW:
c -= psmax;
e -= psmax; }
if (a > e) continue;
if (b < c) continue;
if (ts[i].genetype != tmRNA) continue;
if (ts[i].comp != comp) continue;
score = (a >= c)?((b >= e)?e-a:thresh):((b >= e)?thresh:b-c);
if (score >= smax)
if (score > smax)
{ n = i;
smax = score; }
else
if (ts[i].energy < ts[n].energy)
n = i; }
a -= psmax;
b -= psmax; }
for (i = 0; i < nt; i++)
{ c = ts[i].start;
e = ts[i].stop;
if (e < c)
{ e += psmax;
if (a > e) goto NXTN;
if (b < c) goto NXTN;
if (ts[i].genetype != tmRNA) continue;
if (ts[i].comp != comp) continue;
score = (a >= c)?((b >= e)?e-a:thresh):((b >= e)?thresh:b-c);
if (score >= smax)
if (score > smax)
{ n = i;
smax = score; }
else
if (ts[i].energy < ts[n].energy)
n = i;
NXTN:
c -= psmax;
e -= psmax; }
if (a > e) continue;
if (b < c) continue;
if (ts[i].genetype != tmRNA) continue;
if (ts[i].comp != comp) continue;
score = (a >= c)?((b >= e)?e-a:thresh):((b >= e)?thresh:b-c);
if (score >= smax)
if (score > smax)
{ n = i;
smax = score; }
else
if (ts[i].energy < ts[n].energy)
n = i; }
if ((10*smax) > (9*thresh)) return(ts + n);
return(NULL); }
void overlap(data_set *d, int sort[], int n, int it, csw *sw)
{ int i,j,flag,cross,crosstoo;
long a,b,e,f,a2,b2,e2,f2,psmax;
char sname[100],s[100];
flag = 0;
cross = 0;
psmax = d->psmax;
a = ts[it].start;
b = ts[it].stop;
if (b < a)
{ a2 = a - psmax;
b2 = b;
b += psmax;
cross = 1; }
j = -1;
while (++j < n)
{ i = sort[j];
if (i == it) continue;
e = ts[i].start;
f = ts[i].stop;
crosstoo = 0;
if (f < e)
{ e2 = e - psmax;
f2 = f;
f += psmax;
crosstoo = 1; }
if (a <= f)
if (b >= e)
goto OV;
if (crosstoo)
if (a <= f2)
if (b >= e2)
goto OV;
if (cross)
{ if (a2 <= f)
if (b2 >= e)
goto OV;
if (crosstoo)
if (a2 <= f2)
if (b2 >= e2)
goto OV; }
continue;
OV:
if (!flag) fputc('\n',sw->f);
name(ts+i,sname,1,sw);
location(s,ts+i,sw,sname);
fprintf(sw->f,"Overlap with %d: %s\n", j+1,s);
flag = 1; }
if (flag) fputc('\n',sw->f); }
void init_gene(int nstart, int nstop)
{ int i;
for (i = nstart; i < nstop; i++)
{ ts[i].energy = -1.0;
ts[i].genetype = noGENE;
ts[i].tps = 0;
*(ts[i].name) = '\0'; }}
gene *find_slot(data_set *d, gene *t, int *nts, csw *sw)
{ int i,newspace;
char s1[80],s2[80],s3[80],s4[80];
gene *tn,*tsn;
if (sw->comp)
{ t->stop = sw->start - t->start - 1;
t->start = t->stop - t->nbase - t->nintron + 1;
t->comp = 1; }
else
{ t->start += sw->start;
t->stop = t->start + t->nbase + t->nintron - 1;
t->comp = 0; }
if (!sw->linear)
{ t->start = sq(t->start);
t->stop = sq(t->stop); }
if (t->genetype == tRNA)
tn = nearest_trna_gene(d,*nts,t,sw);
else
if (t->genetype == tmRNA)
tn = nearest_tmrna_gene(d,*nts,t);
else tn = NULL;
if (tn)
{ if (t->energy <= tn->energy) return(NULL);
copy(tn->name,t->name);
if (sw->verbose)
{ fprintf(stderr,"%s %s ",name(t,s1,0,sw),position(s3,t,sw));
if (sw->energydisp) fprintf(stderr,"(%g) ",nenergy(t,sw));
fprintf(stderr,"replacing %s %s",name(tn,s2,1,sw),
position(s4,tn,sw));
if (sw->energydisp) fprintf(stderr," (%g)",nenergy(tn,sw));
fprintf(stderr,"\n"); }}
else
{ if (*nts >= sw->genespace)
{ newspace = (d->ps > 0)?(sw->genespace*(1 + d->psmax/d->ps)):
(sw->genespace + NT);
tsn = (gene *)realloc((void *)ts,newspace*sizeof(gene));
if (tsn == NULL)
{ fprintf(stderr,"No more memory to store detected genes\n");
fprintf(stderr,"Gene lost\n");
return(NULL); }
if (sw->verbose)
fprintf(stderr,
"Expanding detected gene store from %d genes to %d genes\n",
sw->genespace,newspace);
ts = tsn;
init_gene(sw->genespace,newspace);
sw->genespace = newspace; }
copy3cr(d->seqname,t->name,79);
tn = ts + (*nts);
*nts = (*nts) + 1;
if (sw->verbose)
{ fprintf(stderr,"%s at %s",name(t,s1,0,sw),position(s2,t,sw));
if (sw->energydisp) fprintf(stderr," (%g)",nenergy(t,sw));
fprintf(stderr,"\n"); }}
return(tn); }
int aatail(int *s, int *ext, csw *sw)
{ int score,e;
static int A[6] = { 1,0,0,0,0,0 };
static int C[6] = { 0,1,0,0,0,0 };
if (sw->aataildiv)
{ score = 0;
e = 0;
if (A[s[3]])
{ score++;
e = 3; }
if (C[s[2]])
{ score++;
if (!e) e = 2; }
if (C[s[1]])
{ score++;
if (!e) e = 1; }
if (score < 2)
if (A[*s]) score++;
*ext = ++e;
return(score); }
else
{ score = 1;
e = 1;
if (C[s[1]])
{ score++;
e = 2;
if (C[s[2]])
{ score++;
e = 3;
if (A[s[3]])
{ score++;
e = 4; }}}
*ext = e;
return(score); }}
int find_mt_trna(data_set *d, int *seq, int lseq, int nts, csw *sw)
{ int nah,ndh,nch,nth,ncdsh,h,i,j,k,n,p,y,av,gcc,cgcc,catc,athresh;
int igc,nbase,b8,b9,b48,b57,nc,na,nt,nti,nd,ndi,dposmap[32];
int dl,tl,extastem,astem8,astem8d,ti,di,ser,tastem,tastem8,tastem8d;
int astem,asteme,as,as8,aext,aext8,nbasefext,cloop,dloop,tloop,tc;
int carm,cstem,darm,dstem,tarm,tstem,var,varbp,spacer1,spacer2,anticodon;
int ds,dstemmotif,cloop7,mtxdetect,incds;
int *s,*sl,*s1,*s2,*s4,*sa,*sb,*sc,*se,*sf,*sg,*si;
int *slm,*slm1,*sle,*slb,*sld,*sge;
int *dpos,*cpos,*cend,*tpos,*tend,*apos1,*apos2,*aend1,*aend2;
int *clooppos,*cloopend;
unsigned int bondtype,abondtype,mabondtype,acbondtype,cbondtype;
unsigned int agcat,cgcat,tgcat,dbondtype,dtbondtype,tbondtype;
unsigned int r,ct[6],cm,cv,q,tendmap[63];
double gcv,e,ec,ea,eas,ed,et,ev,energy,stem_energy;
double darmthresh,tarmthresh,tthresh,dthresh,dtthresh,thresh;
mt_trna_cloop chit[6];
static mt_trna_loop dhit[mtND+1];
static mt_trna_tloop thit[mtNTH+1];
static mt_trna_astem ahit[mtNA+1];
static mt_cds cdshit[mtNCDS];
gene *tn;
static gene te =
{ "",{TERM},{TERM},NULL,0,0,0L,0L,7,7,1,2,1,4,7,5,7,0,0,0,5,0,5,7,
tRNA,0.0,0,0,0 };
static int cAI[6] = { 8,0,0,0,8,0 };
static int cfCI[6] = { 0,16,0,0,16,0 };
static int cRI[6] = { 8,0,4,0,8,0 };
static int cTI[6] = { 0,0,0,16,16,0 };
static int cYI[6] = { 0,8,0,4,8,0 };
static int AI[6] = { 1,0,0,0,1,0 };
static int CI[6] = { 0,1,0,0,1,0 };
static int GI[6] = { 0,0,1,0,1,0 };
static int TI[6] = { 0,0,0,1,1,0 };
static int RI[6] = { 1,0,1,0,1,0 };
static int YI[6] = { 0,1,0,1,1,0 };
static int WI[6] = { 1,0,0,1,1,0 };
static unsigned int template[6] = { 0,0,0,0,0,0 };
static unsigned int At[6] = { 0,0,0,1,1,0 };
static unsigned int Ct[6] = { 0,0,1,0,1,0 };
static unsigned int Gt[6] = { 0,1,0,1,1,0 };
static unsigned int Tt[6] = { 1,0,1,0,1,0 };
static unsigned int cAt[6] = { 0,0,0,2,2,0 };
static unsigned int cCt[6] = { 0,0,2,0,2,0 };
static unsigned int cGt[6] = { 0,2,0,1,2,0 };
static unsigned int cTt[6] = { 2,0,1,0,2,0 };
static unsigned int aAt[6] = { 0,0,1,2,2,0 };
static unsigned int aCt[6] = { 0,0,2,0,2,0 };
static unsigned int aGt[6] = { 1,2,0,1,2,0 };
static unsigned int aTt[6] = { 2,0,1,1,2,0 };
static unsigned int dAt[6] = { 0,0,1,2,2,0 };
static unsigned int dCt[6] = { 0,0,2,0,2,0 };
static unsigned int dGt[6] = { 1,2,0,2,2,0 };
static unsigned int dTt[6] = { 2,0,2,1,2,0 };
static unsigned int clmotif[mtNCLM] =
{ 0x1321300,0x3321300,0x1323002 };
static int dloopi[mt_DRLmaxlength+1][4] =
{ { -1 }, { -1 }, { -1 }, { -1 }, { -1 }, { -1 }, { -1 },
{ 0,2,-1 }, { 0,2,-1 }, { 0,2,3,-1 }, { 0,3,-1 }, { 0,3,-1 },
{ 0,3,4,-1 }, { 0,4,-1 }, { 0,5,-1 }, { 0,5,6,-1 }, { 0,5,6,-1 } };
static int tloopa[12][4] =
{ { -1 }, { -1 }, { -1 }, { 0,1,-1 }, { 0,2,1,-1 }, { 4,3,2,-1 },
{ 4,3,-1 }, { 4,3,-1 }, { 4,3,-1 }, { 5,4,3,-1 }, { 5,4,-1 }, { 5,-1 } };
static double dA[6] = { 1.0,0.0,0.0,0.0,1.0,0.0 };
static double dT[6] = { 0.0,0.0,0.0,1.0,1.0,0.0 };
static double C[6] = { 0.0,1.0,0.0,0.0,1.0,0.0 };
static double G[6] = { 0.0,0.0,1.0,0.0,1.0,0.0 };
static double T[6] = { 0.0,0.0,0.0,1.0,1.0,0.0 };
static double AX[6] = { 0.0,-1.0,-1.0,-1.0,0.0,-1.0 };
static double AX37[6] = { 0.0,-4.0,-1.0,-4.0,0.0,-4.0 };
static double AXX[6] = { 0.0,-3.0,-1.5,-3.0,0.0,-3.0 };
static double AXX37[6] = { 0.0,-4.0,-4.0,-4.0,0.0,-4.0 };
static double AX7[6] = { 0.0,-0.7,-0.7,-0.7,0.0,-0.7 };
static double CX[6] = { -2.0,0.0,-2.0,-1.0,0.0,-2.0 };
static double CXX[6] = { -4.0,0.0,-4.0,-2.0,0.0,-4.0 };
static double CX7[6] = { -0.7,0.0,-0.7,-0.7,0.0,-0.7 };
static double TX[6] = { -1.0,-1.0,-1.0,0.0,0.0,-1.0 };
static double TXX[6] = { -2.0,-2.0,-2.0,0.0,0.0,-2.0 };
static double YX[6] = { -1.0,0.0,-1.0,0.0,0.0,-1.0 };
static double tC[6] = { 0.0,0.01,0.0,0.0,0.01,0.0 };
static double tG[6] = { 0.0,0.0,0.01,0.0,0.01,0.0 };
static double tT[6] = { 0.0,0.0,0.0,0.01,0.01,0.0 };
static double cA[6] = { 0.8,0.0,0.0,0.0,0.8,0.0 };
static double cfC[6] = { 0.0,2.6,0.0,0.0,2.6,0.0 };
static double cR[6] = { 0.8,-2.0,0.8,-0.8,0.8,-0.8 };
static double cT[6] = { -0.8,0.0,-0.8,2.6,2.6,-0.8 };
static double cY[6] = { -0.8,0.8,-0.8,0.8,0.8,-0.8 };
static double loop_stab[41] =
{ 10.0,2.0,1.0,0.4,0.3,0.2,0.1,0.0,0.1,0.2,0.3,0.4,0.5,1.6,1.7,1.8,
1.9,2.0,2.1,2.2,2.3,3.9,4.0,4.1,4.2,4.3,4.4,4.5,4.6,4.7,4.8,4.9,
5.0,5.1,5.2,5.3,5.4,5.5,5.6,5.7 };
static double bem[6][6] =
{ { mtNOBOND, mtNOBOND, mtGABOND, mtATBOND, mtATBOND, mtNOBOND },
{ mtNOBOND, mtNOBOND, mtGCBOND, mtNOBOND, mtGCBOND, mtNOBOND },
{ mtGABOND, mtGCBOND, mtGGBOND, mtGTBOND, mtGCBOND, mtNOBOND },
{ mtATBOND, mtNOBOND, mtGTBOND, mtTTBOND, mtATBOND, mtNOBOND },
{ mtATBOND, mtGCBOND, mtGCBOND, mtATBOND, mtGCBOND, mtNOBOND },
{ mtNOBOND, mtNOBOND, mtNOBOND, mtNOBOND, mtNOBOND, mtNOBOND } };
static double hbem[5][5] =
{ { 0.0,0.0,0.0,mtBONDSTAB+0.5*mtATBOND,mtBONDSTAB+0.5*mtATBOND },
{ 0.0,0.0,mtBONDSTAB+0.5*mtGCBOND,0.0,mtBONDSTAB+0.5*mtGCBOND },
{ 0.0,mtBONDSTAB+0.5*mtGCBOND,0.0,mtBONDSTAB+0.5*mtGTBOND,
mtBONDSTAB+0.5*mtGCBOND },
{ mtBONDSTAB+0.5*mtATBOND,0.0,mtBONDSTAB+0.5*mtGTBOND,0.0,
mtBONDSTAB+0.5*mtATBOND },
{ mtBONDSTAB+0.5*mtATBOND,mtBONDSTAB+0.5*mtGCBOND,
mtBONDSTAB+0.5*mtGCBOND,
mtBONDSTAB+0.5*mtATBOND,
mtBONDSTAB+0.5*mtGCBOND } };
tarmthresh = sw->mttarmthresh;
tthresh = sw->mttthresh;
dthresh = sw->mtdthresh;
dtthresh = sw->mtdtthresh;
ds = sw->discrim;
extastem = sw->extastem;
cloop7 = sw->cloop7;
mtxdetect = sw->mtxdetect;
/* find coding sequences */
ncdsh = 0;
/* find cstems */
sc = seq + sw->loffset;
sl = seq + lseq - sw->roffset;
h = sc[16];
p = sc[15];
j = sc[14];
k = sc[13];
n = sc[12];
y = sc[11];
ct[0] = cAt[h]|(cAt[p]<<4)|(cAt[j]<<8)|(cAt[k]<<12)|
(cAt[n]<<16)|(cAt[y]<<20);
ct[1] = cCt[h]|(cCt[p]<<4)|(cCt[j]<<8)|(cCt[k]<<12)|
(cCt[n]<<16)|(cCt[y]<<20);
ct[2] = cGt[h]|(cGt[p]<<4)|(cGt[j]<<8)|(cGt[k]<<12)|
(cGt[n]<<16)|(cGt[y]<<20);
ct[3] = cTt[h]|(cTt[p]<<4)|(cTt[j]<<8)|(cTt[k]<<12)|
(cTt[n]<<16)|(cTt[y]<<20);
ct[4] = 0;
ct[5] = 0;
for (; sc < sl; sc++)
{ p = sc[17];
ct[0] = (ct[0] << 4) | cAt[p];
ct[1] = (ct[1] << 4) | cCt[p];
ct[2] = (ct[2] << 4) | cGt[p];
ct[3] = (ct[3] << 4) | cTt[p];
cm = (ct[sc[4]] >> 16) + (ct[sc[3]] >> 12) + (ct[sc[2]] >> 8) +
(ct[sc[1]] >> 4) + ct[*sc];
/* 7 base cloop */
cv = (cm & 0xf0);
athresh = 12;
nch = 0;
/* exclude the following cloops */
/* RRnnnNN, NRnnnYN */
/* NRnnnNN with cstem < 3 Watson-Crick basepairs or equivalent */
/* RYnnnYN */
/* NYnnnNN with cstem < 1 Watson-Crick basepair or equivalent */
/* NYnnnNN with cstem < 2 Watson-Crick basepairs or equivalent */
/* unless cloop = CTnnnAN */
if (RI[sc[6]])
{ if (RI[sc[5]]) goto CLOOP6;
if (YI[sc[10]]) goto CLOOP6;
if (cv < 0x60) goto CLOOP6; }
else
{ if (YI[sc[10]])
if (RI[sc[5]]) goto CLOOP6;
if (cv < 0x40)
{ if (cv < 0x20) goto CLOOP6;
if (sc[5] != Cytosine) goto CLOOP6;
if (sc[6] != Thymine) goto CLOOP6;
if (sc[10] != Adenine) goto CLOOP6;
athresh = 11; }
else if (cv < 0x70)
{ athresh = 11;
k = cYI[sc[5]] + cTI[sc[6]] + cRI[sc[10]] + cAI[sc[11]];
if (sc[6] == Cytosine)
if (sc[5] == Cytosine)
k += 16;
else
if (sc[5] == Thymine)
if (sc[11] == Adenine)
k += 16;
if (cv == 0x40)
{ if (k < 40) goto CLOOP6; }
else
if (cv == 0x50)
{ if (k < 28) goto CLOOP6; }
else
{ if (k < 20) goto CLOOP6;
athresh = 9; }}
else
athresh = (cv < 10)?9:8; }
chit[0].pos = sc;
chit[0].stem = 5;
chit[0].loop = 7;
chit[0].looppos = sc + 5;
chit[0].arm = 17;
chit[0].end = sc + 17;
chit[0].anticodon = (sc[7] << 4) + (sc[8] << 2) + sc[9];
if (bp[sc[-1]][sc[17]])
{ chit[1].pos = sc-1;
chit[1].stem = 6;
chit[1].loop = 7;
chit[1].looppos = sc + 5;
chit[1].arm = 19;
chit[1].end = sc + 18;
chit[1].anticodon = chit[0].anticodon;
nch = 2; }
else nch = 1;
/* 6 base cloop */
/* exclude cstem < 4 Watson-Crick basepairs or equivalent */
/* exclude cloop = RRnnNN */
/* exclude cloop = NNnnYY */
CLOOP6:
if (cloop7) goto CLOOPE;
if ((cm & 0xf00) >= 0x800)
{ if (!YI[sc[6]])
if (!YI[sc[5]])
goto CLOOP8;
if (!RI[sc[9]])
if (!RI[sc[10]])
goto CLOOP8;
se = sc + 20;
sg = sc;
while (sg < se)
{ sf = sg + 5;
while (sf < (sg + 11))
{ if (*sf == *sg)
if (sf[1] == sg[1])
if (sf[2] == sg[2])
if (sf[3] == sg[3])
if (sf[4] == sg[4])
{ sb = sg + 5;
s = sf + 5;
i = 0;
while (sb < sf)
if (*sb++ != *s++)
if (++i > 1) goto NXSEG6;
goto CLOOPE; }
NXSEG6:
sf++; }
sg++; }
chit[nch].pos = sc;
chit[nch].stem = 5;
chit[nch].loop = 6;
chit[nch].looppos = sc + 5;
chit[nch].arm = 16;
chit[nch].end = sc + 16;
chit[nch++].anticodon = 0;
if (athresh > 10) athresh = 10;
if (bp[sc[-1]][sc[16]])
{ chit[nch].pos = sc-1;
chit[nch].stem = 6;
chit[nch].loop = 6;
chit[nch].looppos = sc + 5;
chit[nch].arm = 18;
chit[nch].end = sc + 17;
chit[nch++].anticodon = 0; }}
/* 8 base cloop */
/* exclude cstem < 4 Watson-Crick basepairs or equivalent */
/* exclude cloop = RRnnnnNN */
/* exclude cloop = NNnnnnYY */
CLOOP8:
if ((cm & 0xf) >= 0x8)
{ if (!YI[sc[5]])
if (!YI[sc[6]])
goto CLOOPE;
if (!RI[sc[12]])
if (!RI[sc[11]])
goto CLOOPE;
se = sc + 20;
sg = sc;
while (sg < se)
{ sf = sg + 5;
while (sf < (sg + 11))
{ if (*sf == *sg)
if (sf[1] == sg[1])
if (sf[2] == sg[2])
if (sf[3] == sg[3])
if (sf[4] == sg[4])
{ sb = sg + 5;
s = sf + 5;
i = 0;
while (sb < sf)
if (*sb++ != *s++)
if (++i > 1) goto NXSEG8;
goto CLOOPE; }
NXSEG8:
sf++; }
sg++; }
chit[nch].pos = sc;
chit[nch].stem = 5;
chit[nch].loop = 8;
chit[nch].looppos = sc + 5;
chit[nch].arm = 18;
chit[nch].end = sc + 18;
chit[nch++].anticodon = 0;
if (athresh > 10) athresh = 10;
if (bp[sc[-1]][sc[18]])
{ chit[nch].pos = sc-1;
chit[nch].stem = 6;
chit[nch].loop = 8;
chit[nch].looppos = sc + 5;
chit[nch].arm = 20;
chit[nch].end = sc + 19;
chit[nch++].anticodon = 0; }}
/* calculate carm energy */
CLOOPE:
if (nch < 1) continue;
for (nc = 0; nc < nch; nc++)
{ s1 = chit[nc].pos;
cstem = chit[nc].stem;
cloop = chit[nc].loop;
s4 = s1 + cstem;
s2 = s4 + cloop;
energy = (cloop == 7)?0.0:-4.0;
energy += cY[*s4] + cT[s4[1]] + cR[s2[-2]] + cA[s2[-1]];
if (s4[1] == Cytosine)
if (*s4 == Cytosine)
energy += 2.6;
else
if (*s4 == Thymine)
if (s2[-1] == Adenine)
energy += 2.6;
s2 += cstem;
stem_energy = bem[*s1][*--s2];
k = neighbour_map[*s1][*s2];
stem_energy += neighbour_em[k][s1[1]][s2[-1]];
bondtype = btmap[*s1][*s2];
if (bp[*s1][*s2])
{ if (assymst[s2[1]][s1[-1]]) stem_energy += mtTERMSTAB;
else stem_energy += send_em[*s2][*s1]; }
else
{ if (assymst[*s2][*s1]) stem_energy += mtTERMSTAB;
else stem_energy += send_em[s2[-1]][s1[1]]; }
while (++s1 < s4)
{ if (!wcbp[*s1][*--s2])
{ if (!wcbp[s1[-1]][s2[1]])
{ for (j = 0; j < mtNTM; j++)
if (*s1 == tandemid[j][1])
if (*s2 == tandemid[j][3])
if (s1[-1] == tandemid[j][0])
if (s2[1] == tandemid[j][2])
{ stem_energy += tandem_em[j];
break; }
if (s1 < (s4-1))
if (!bp[s1[1]][s2[-1]]) stem_energy -= mt3MMSTAB; }
k = neighbour_map[*s1][*s2];
stem_energy += (neighbour_em[k][s1[-1]][s2[1]] +
neighbour_em[k][s1[1]][s2[-1]]); }
bondtype += btmap[*s1][*s2];
stem_energy += bem[*s1][*s2]; }
if (!bp[*--s1][*s2])
{ s1--;
s2++; }
if (assymst[s1[1]][s2[-1]]) stem_energy += mtTERMSTAB;
else stem_energy += send_em[*s1][*s2];
cgcc = bondtype & 0xf;
if (cgcc <= 0)
{ catc = (bondtype & 0xf0) >> 4;
if (catc < cstem) energy -= mtGCPENALTY; }
if (cstem == 6) energy += 1.0;
chit[nc].bondtype = bondtype;
chit[nc].stem_energy = stem_energy;
chit[nc].energy = energy + stem_energy; }
/* find tarms */
nth = 0;
slm = sc + 61;
sle = sc + 57;
sb = sc + 21;
sg = sc + 16;
sge = sg + 30;
slb = sg + 32;
template[0] = At[*slm];
template[1] = Ct[*slm];
template[2] = Gt[*slm];
template[3] = Tt[*slm];
while (--slm > sle)
{ template[0] = (template[0] << 4) | At[*slm];
template[1] = (template[1] << 4) | Ct[*slm];
template[2] = (template[2] << 4) | Gt[*slm];
template[3] = (template[3] << 4) | Tt[*slm]; }
while (slm >= sb)
{ template[0] = ((template[0] << 4) | At[*slm]) & 0xfffff;
template[1] = ((template[1] << 4) | Ct[*slm]) & 0xfffff;
template[2] = ((template[2] << 4) | Gt[*slm]) & 0xfffff;
template[3] = ((template[3] << 4) | Tt[*slm]) & 0xfffff;
sf = slm + 3;
if (sf > sge) sf = sge;
apos2 = slm + 5;
si = sg;
s = si + 4;
r = template[*si];
while (++si < s) r = (r >> 4) + template[*si];
while (si <= sf)
{ if (si < slm)
r = (r >> 4) + template[*si++];
else
{ si++;
r = r >> 4; }
q = r & 0xf;
if (slm > slb)
{ if (q < 5) continue;
tloop = (int)(slm - si); }
else
{ if (q < 2) continue;
if (q < 3)
{ if (!wcbp[si[-5]][apos2[-1]]) continue;
if (!wcbp[si[-4]][apos2[-2]]) continue;
tloop = (int)(slm - si);
if (tloop > 5) continue; }
else
{ tloop = (int)(slm - si);
if (q < 4)
if (!bp[si[-4]][apos2[-2]])
if (!bp[si[-2]][apos2[-4]])
{ if (tloop < 4) continue;
if (si[-1] != Guanine) continue;
if (*si != Thymine) continue;
if (si[1] != Thymine) continue; }}}
if (tloop < 7)
{ if (tloop < 2)
if (tloop <= 0)
{ if (tloop <= -2)
{ if (!wcbp[si[-5]][apos2[-1]]) continue;
if (!wcbp[si[-4]][apos2[-2]]) continue;
tstem = 2;
tloop += 6; }
else
if (bp[si[-3]][apos2[-3]])
{ tstem = 3;
tloop += 4; }
else
{ if (!wcbp[si[-5]][apos2[-1]]) continue;
if (!wcbp[si[-4]][apos2[-2]]) continue;
tstem = 2;
tloop += 6; }}
else
{ if (bp[si[-2]][apos2[-4]])
{ tstem = 4;
tloop += 2; }
else
if (bp[si[-3]][apos2[-3]])
{ tstem = 3;
tloop += 4; }
else
{ if (!wcbp[si[-5]][apos2[-1]]) continue;
if (!wcbp[si[-4]][apos2[-2]]) continue;
tstem = 2;
tloop += 6; }}
else
{ if (bp[si[-1]][apos2[-5]])
{ if (q != 4) tstem = 5;
else
{ if (bp[si[-2]][apos2[-4]]) tstem = 5;
else
{ k = GI[si[-3]] + TI[si[-2]] + TI[si[-1]] + CI[*si];
if (k >= 2)
{ tstem = 3;
tloop += 4; }
else tstem = 5; }}}
else
{ if (bp[si[-2]][apos2[-4]])
{ tstem = 4;
tloop += 2; }
else
if (bp[si[-3]][apos2[-3]])
{ tstem = 3;
tloop += 4; }
else
{ if (!wcbp[si[-5]][apos2[-1]]) continue;
if (!wcbp[si[-4]][apos2[-2]]) continue;
tstem = 2;
tloop += 6; }
}}
if (tloop < 3)
if (tstem > 3)
{ tstem--;
tloop += 2; }}
else
{ if (!bp[si[-1]][apos2[-5]])
if (!bp[si[-2]][apos2[-4]])
{ tstem = 3;
tloop += 4; }
else
{ tstem = 4;
tloop += 2; }
else tstem = 5; }
if (tloop > 17)
if (tstem < 5)
continue;
/* calculate tarm energy */
s1 = si - 5;
tpos = s1;
s4 = s1 + tstem;
s2 = apos2;
if (tt[*s1][*--s2])
{ energy = mtTSTTSTAB;
if (tt[*++s1][*--s2])
{ energy += mtTSTTSTAB;
bondtype = btmap[*s1++][*s2--]; }
else bondtype = 0; }
else
{ energy = 0.0;
bondtype = 0; }
/* calculate tstem energy */
stem_energy = bem[*s1][*s2];
k = neighbour_map[*s1][*s2];
stem_energy += neighbour_em[k][s1[1]][s2[-1]];
bondtype += btmap[*s1][*s2];
while (++s1 < s4)
{ if (!wcbp[*s1][*--s2])
{ if (!wcbp[s1[-1]][s2[1]])
{ for (j = 0; j < mtNTM; j++)
if (*s1 == tandemid[j][1])
if (*s2 == tandemid[j][3])
if (s1[-1] == tandemid[j][0])
if (s2[1] == tandemid[j][2])
{ stem_energy += tandem_em[j];
break; }
if (s1 < (s4-1))
if (!bp[s1[1]][s2[-1]]) stem_energy -= mt3MMSTAB; }
k = neighbour_map[*s1][*s2];
stem_energy += (neighbour_em[k][s1[-1]][s2[1]] +
neighbour_em[k][s1[1]][s2[-1]]); }
bondtype += btmap[*s1][*s2];
stem_energy += bem[*s1][*s2]; }
s1--;
if (tloop < 4) stem_energy += ssend_em[*s1][*s2];
else
if (assymst[s1[1]][s2[-1]]) stem_energy += mtTERMSTAB;
else stem_energy += send_em[*s1][*s2];
/* compile possible tarms */
energy += (stem_energy - mtBONDSTAB*(double)(5-tstem));
if (energy >= tarmthresh)
{ thit[nth].pos = tpos;
s1 = tpos + tstem;
s2 = apos2 - tstem;
thit[nth].energy = energy - loop_stab[tloop] +
tG[s1[-1]] + tT[*s1] + tT[s1[1]] + tC[s1[2]];
thit[nth].stem_energy = stem_energy;
thit[nth].bondtype = bondtype;
thit[nth].stem = tstem;
thit[nth].loop = tloop;
thit[nth].end = tpos + 2*tstem + tloop;
if (++nth >= mtNTH)
{ fprintf(stderr,"Too many mt-tstem hits\n");
break; }
if (tstem > 2)
if (tloop < 10)
if (gt[s1[-1]][*s2])
{ thit[nth].pos = tpos;
thit[nth].energy = energy - mtBONDSTAB - mtGTBOND -
loop_stab[tloop+2] +
tG[s1[-2]] + tT[s1[-1]] + tT[*s1] + tC[s1[1]];
thit[nth].stem_energy = stem_energy - mtGTBOND;
thit[nth].bondtype = bondtype - 0x100;
thit[nth].stem = tstem - 1;
thit[nth].loop = tloop + 2;
thit[nth].end = thit[nth-1].end;
if (++nth >= mtNTH)
{ fprintf(stderr,"Too many mt-tstem hits\n");
break; }
if (tstem > 3)
if (tloop < 8)
if (gt[s1[-2]][s2[1]])
{ thit[nth].pos = tpos;
thit[nth].energy = energy - 2.0*mtBONDSTAB - 2.0*mtGTBOND -
loop_stab[tloop+4] + tG[s1[-3]] +
tT[s1[-2]] + tT[s1[-1]] + tC[*s1];
thit[nth].stem_energy = stem_energy - 2.0*mtGTBOND;
thit[nth].bondtype = bondtype - 0x200;
thit[nth].stem = tstem - 2;
thit[nth].loop = tloop + 4;
thit[nth].end = thit[nth-1].end;
if (++nth >= mtNTH)
{ fprintf(stderr,"Too many mt-tstem hits\n");
break; }}}
if (tstem < 5)
{ if (tloop < 11) continue;
if (tloop > 16) continue;
if (!wcbp[s1[1]][s2[-2]]) continue;
bondtype += btmap[*s1][s2[-1]] + btmap[s1[1]][s2[-2]];
tstem += 2;
tloop -= 4; }
else
{ if (tloop < 9) continue;
if (wcbp[*s1][s2[-1]])
{ if (tloop > 14) continue;
tstem++;
tloop -= 2;
bondtype += btmap[*s1][s2[-1]]; }
else
{ if (tloop < 11) continue;
if (tloop > 16) continue;
if (!wcbp[s1[1]][s2[-2]]) continue;
bondtype += btmap[*s1][s2[-1]] + btmap[s1[1]][s2[-2]];
tstem += 2;
tloop -= 4; }}
thit[nth].pos = tpos;
s1 = tpos + tstem;
thit[nth].energy = energy - loop_stab[tloop] +
tG[s1[-1]] + tT[*s1] + tT[s1[1]] + tC[s1[2]];
thit[nth].stem_energy = stem_energy;
thit[nth].bondtype = bondtype;
thit[nth].stem = tstem;
thit[nth].loop = tloop;
thit[nth].end = thit[nth-1].end;
if (++nth >= mtNTH)
{ fprintf(stderr,"Too many mt-tstem hits\n");
break; }
if (tloop < 9) continue;
if (!wcbp[*s1][apos2[-tstem-1]]) continue;
if (++tstem > 7) continue;
if (tloop > 14) continue;
tloop -= 2;
thit[nth].pos = tpos;
s1 = tpos + tstem;
thit[nth].energy = energy - loop_stab[tloop] +
tG[s1[-1]] + tT[*s1] + tT[s1[1]] + tC[s1[2]];
thit[nth].stem_energy = stem_energy;
thit[nth].bondtype = bondtype;
thit[nth].stem = tstem;
thit[nth].loop = tloop;
thit[nth].end = thit[nth-1].end;
if (++nth >= mtNTH)
{ fprintf(stderr,"Too many mt-tstem hits\n");
break; }}}
slm--; }
/* find darms */
ndh = 0;
sle = sc - 4;
slb = sc - 8;
slm = sc - 1;
template[0] = dAt[*slm];
template[1] = dCt[*slm];
template[2] = dGt[*slm];
template[3] = dTt[*slm];
while (--slm > sle)
{ template[0] = (template[0] << 4) | dAt[*slm];
template[1] = (template[1] << 4) | dCt[*slm];
template[2] = (template[2] << 4) | dGt[*slm];
template[3] = (template[3] << 4) | dTt[*slm]; }
slm1 = slm;
while (slm > slb)
{ template[0] = ((template[0] << 4) | dAt[*slm]) & 0xffff;
template[1] = ((template[1] << 4) | dCt[*slm]) & 0xffff;
template[2] = ((template[2] << 4) | dGt[*slm]) & 0xffff;
template[3] = ((template[3] << 4) | dTt[*slm]) & 0xffff;
slm--;
si = slm - 18;
s = si + 3;
r = template[*si];
while (++si < s) r = (r >> 4) + template[*si];
while (si <= slm1)
{ if (si < slm) r = (r >> 4) + template[*si++];
else
{ r = r >> 4;
si++; }
if ((q = (r & 0xf)) < 6)
{ q += (unsigned int)(TI[si[-6]] + RI[si[-5]]);
if (q < 6) continue; }
/* calculate darm energy */
s1 = si - 4;
dhit[ndh].pos = s1;
energy = dT[s1[-2]] + dA[s1[-1]];
dloop = (int)(slm1 - si);
if (dloop > 2)
if (bp[si[-1]][*slm1])
{ dstem = 4;
goto EC; }
if (dloop > 0)
if ((ggstembp[si[-2]][slm[2]]) || (gabp[si[-1]][*slm1]))
{ dstem = 3;
dloop += 2;
energy += mtNOBOND;
goto EC; }
if (!wcbp[si[-3]][slm[3]]) continue;
if (!gc[si[-4]][slm[4]]) continue;
dstem = 2;
dloop += 4;
if (dloop > 5) energy += mtNOBOND;
energy += mtNOBOND;
EC:
s2 = slm + 4;
s4 = s1 + dstem;
if (!wcbp[s1[1]][s2[-1]])
if (stemterm[s1[1]][s2[-1]]) energy -= 1.0;
else
if (bp[s1[1]][s2[-1]]) energy -= 1.5;
else energy -= 2.0;
/* calculate dstem energy */
stem_energy = bem[*s1][*s2];
k = neighbour_map[*s1][*s2];
stem_energy += neighbour_em[k][s1[1]][s2[-1]];
bondtype = btmap[*s1][*s2];
if (bp[*s1][*s2])
{ if (assymst[s2[1]][s1[-1]]) stem_energy += mtTERMSTAB;
else stem_energy += send_em[*s2][*s1];
s1++;
s2--; }
else
{ s1++;
s2--;
if (assymst[s2[1]][s1[-1]]) stem_energy += mtTERMSTAB;
else stem_energy += send_em[*s2][*s1]; }
stem_energy += bem[*s1][*s2];
k = neighbour_map[*s1][*s2];
stem_energy += (neighbour_em[k][s1[-1]][s2[1]] +
neighbour_em[k][s1[1]][s2[-1]]);
bondtype += btmap[*s1][*s2];
while (++s1 < s4)
{ if (!wcbp[*s1][*--s2])
{ if (!wcbp[s1[-1]][s2[1]])
{ for (j = 0; j < mtNTM; j++)
if (*s1 == tandemid[j][1])
if (*s2 == tandemid[j][3])
if (s1[-1] == tandemid[j][0])
if (s2[1] == tandemid[j][2])
{ stem_energy += tandem_em[j];
break; }
if (s1 < (s4-1))
if (!bp[s1[1]][s2[-1]]) stem_energy -= mt3MMSTAB; }
k = neighbour_map[*s1][*s2];
stem_energy += (neighbour_em[k][s1[-1]][s2[1]] +
neighbour_em[k][s1[1]][s2[-1]]); }
bondtype += btmap[*s1][*s2];
stem_energy += bem[*s1][*s2]; }
if (!bp[*--s1][*s2])
{ s1--;
s2++; }
if (dloop < 4) stem_energy += ssend_em[*s1][*s2];
else
if (assymst[s1[1]][s2[-1]]) stem_energy += mtTERMSTAB;
else stem_energy += send_em[*s1][*s2];
/* compile possible darms */
energy += stem_energy;
dhit[ndh].energy = energy;
dhit[ndh].stem_energy = stem_energy;
dhit[ndh].bondtype = bondtype;
dhit[ndh].stem = dstem;
dhit[ndh].loop = dloop;
if (++ndh >= mtND)
{ fprintf(stderr,"Too many mt-dstem hits\n");
break; }
if (dstem == 4)
{ if (dloop >= 6)
if (bondtype < 0x1000)
{ s1 = si - 5;
s2 = slm + 5;
if (bp[*s1][*s2])
{ dhit[ndh].pos = s1;
e = 0.5 + bem[*s1][*s2];
dhit[ndh].energy = energy + e;
if (wcbp[*s1][*s2])
dhit[ndh].energy += (dT[s1[-2]] + dA[s1[-1]] -
dT[s1[-1]] - dA[*s1]);
dhit[ndh].stem_energy = stem_energy + e;
dhit[ndh].bondtype = bondtype + btmap[*s1][*s2];
dhit[ndh].stem = 5;
dhit[ndh].loop = dloop;
if (++ndh >= mtND)
{ fprintf(stderr,"Too many mt-dstem hits\n");
break; }}}}
else
if (dloop >= 6)
{ s1 = si - 1;
s2 = slm1;
if (stemterm[*s1][*s2])
{ dhit[ndh].pos = si - 4;
dhit[ndh].energy = energy;
dhit[ndh].stem_energy = stem_energy;
dhit[ndh].bondtype = bondtype;
dhit[ndh].stem = 4;
dhit[ndh].loop = dloop - 2;
if (++ndh >= mtND)
{ fprintf(stderr,"Too many mt-dstem hits\n");
break; }}}
if (dloop >= 4) continue;
s1 = si - 4 + dstem - 1;
s2 = s1 + dloop + 1;
if (bp[*s1][*s2]) continue;
dhit[ndh].pos = si - 4;
dhit[ndh].energy = energy + 0.001;
dhit[ndh].stem_energy = stem_energy;
dhit[ndh].bondtype = bondtype;
dhit[ndh].stem = dstem - 1;
dhit[ndh].loop = dloop + 2;
if (++ndh >= mtND)
{ fprintf(stderr,"Too many mt-dstem hits\n");
break; } }
slm1--; }
/* build darm exclusion map */
/* 5' astems further from carm than */
/* mt_DRLmaxlength must match a darm */
for (i = 3; i <= 30; i++) dposmap[i] = 0;
sf = sc - mt_DRLmaxlength - 1;
sld = sf;
if (ndh > 0)
{ s = dhit[0].pos;
for (nd = 0; nd < ndh; nd++)
{ se = dhit[nd].pos;
if (se < s) s = se;
i = (int)(sc - se);
if (dposmap[++i] < 1) dposmap[i] = 1;
dposmap[++i] = 2;
if (dposmap[++i] < 1) dposmap[i] = 1; }
s -= 4;
if (s < sf) sf = s; }
/* build tarm exclusion map */
/* 3' astems further from carm than */
/* mt_TVRLmaxlength must match a tarm */
for (i = 17; i <= 62; i++) tendmap[i] = 0;
s2 = sc + mt_TVRLmaxlength + 17;
sle = s2;
if (nth > 0)
{ s = thit[0].end;
for (nt = 0; nt < nth; nt++)
{ se = thit[nt].end;
if (se > s) s = se;
i = (int)(se - sc);
bondtype = thit[nt].bondtype;
if (tendmap[i])
{ if (bondtype < tendmap[i]) tendmap[i] = bondtype; }
else tendmap[i] = bondtype; }
if (s > s2) s2 = s; }
/* find astems in 3 categories: */
/* high energy astems close to carm */
/* high energy astems matching a high energy tarm far from carm */
/* low energy astem matching a darm and tarm */
nah = 0;
sa = sc - 3;
sg = sf - 6;
sb = sc + 17;
se = s2 + 6;
template[0] = aAt[*se];
template[1] = aCt[*se];
template[2] = aGt[*se];
template[3] = aTt[*se];
while (--se > s2)
{ template[0] = (template[0] << 4) | aAt[*se];
template[1] = (template[1] << 4) | aCt[*se];
template[2] = (template[2] << 4) | aGt[*se];
template[3] = (template[3] << 4) | aTt[*se]; }
ti = (int)(se - sc);
while (se >= sb)
{ template[0] = ((template[0] << 4) | aAt[*se]) & 0xfffffff;
template[1] = ((template[1] << 4) | aCt[*se]) & 0xfffffff;
template[2] = ((template[2] << 4) | aGt[*se]) & 0xfffffff;
template[3] = ((template[3] << 4) | aTt[*se]) & 0xfffffff;
if (tendmap[ti])
{ nti = (tendmap[ti] < 0x2000)?1:0; }
else
{ if (se > sle) goto ANX;
nti = -1; }
si = sg;
r = template[*si];
while (++si < sf) r = (r >> 4) + template[*si];
di = (int)(sc - si);
while (si < sa)
{ r = (r >> 4) + template[*si++];
if (dposmap[--di])
{ if (nti <= 0)
{ if (nti < 0)
if (dposmap[di] < 2) continue;
if ((av = (r & 0xf)) < athresh) continue; }}
else
{ if (si < sld) continue;
if (nti < 0) continue;
if ((av = (r & 0xf)) < athresh) continue; }
if (nah >= mtNA)
{ fprintf(stderr,"Too many mt-astem hits\n");
break; }
/* predict astem length and calculate astem energy */
s1 = si - 7;
s2 = se + 6;
if (bp[*s1][*s2])
{ astem = 7;
energy = 0.0;
ahit[nah].pos1 = s1;
ahit[nah].pos2 = se; }
else
if (ggstemterm[*s1][*s2])
{ astem = 7;
ahit[nah].pos1 = s1;
ahit[nah].pos2 = se;
energy = bem[*s1++][*s2--]; }
else
{ energy = bem[*s1++][*s2--];
if (bp[*s1][*s2])
{ astem = 6;
ahit[nah].pos1 = s1;
ahit[nah].pos2 = se; }
else
if (ggstemterm[*s1][*s2])
{ astem = 6;
ahit[nah].pos1 = s1;
ahit[nah].pos2 = se;
energy += bem[*s1++][*s2--]; }
else
{ astem = 5;
energy += bem[*s1++][*s2--];
ahit[nah].pos1 = s1;
ahit[nah].pos2 = se; }}
ahit[nah].stem = astem;
bondtype = btmap[*s1][*s2];
energy += bem[*s1][*s2];
k = neighbour_map[*s1][*s2];
energy += neighbour_em[k][s1[1]][s2[-1]];
energy += bem[*++s1][*--s2];
k = neighbour_map[*s1][*s2];
energy += (neighbour_em[k][s1[-1]][s2[1]] +
neighbour_em[k][s1[1]][s2[-1]]);
bondtype += btmap[*s1][*s2];
while (++s1 < si)
{ if (!wcbp[*s1][*--s2])
{ if (!wcbp[s1[-1]][s2[1]])
{ for (j = 0; j < mtNTM; j++)
if (*s1 == tandemid[j][1])
if (*s2 == tandemid[j][3])
if (s1[-1] == tandemid[j][0])
if (s2[1] == tandemid[j][2])
{ energy += tandem_em[j];
break; }
if (s1 < (si-1))
if (!bp[s1[1]][s2[-1]]) energy -= mt3MMSTAB; }
k = neighbour_map[*s1][*s2];
energy += (neighbour_em[k][s1[-1]][s2[1]] +
neighbour_em[k][s1[1]][s2[-1]]); }
bondtype += btmap[*s1][*s2];
energy += bem[*s1][*s2]; }
if (!bp[*--s1][*s2])
if (!bp[*--s1][*++s2])
if (!bp[*--s1][*++s2])
if (!bp[*--s1][*++s2])
goto NOST;
if (assymst[s1[1]][s2[-1]]) energy += mtTERMSTAB;
NOST:
ahit[nah].energy = energy;
ahit[nah].bondtype = bondtype;
nah++; }
ANX:
se--;
ti--; }
if (nah <= 0) continue;
/* build mttrna genes */
/* cycle through astems first so that */
/* GC content is only calculated once per astem */
thresh = -INACTIVE;
te.ps = NULL;
for (na = 0; na < nah; na++)
{ apos2 = ahit[na].pos2;
apos1 = ahit[na].pos1;
astem = ahit[na].stem;
aend1 = apos1 + astem;
astem8 = (astem == 7)?(wcbp[apos1[-1]][apos2[7]]):0;
asteme = 0;
ea = ahit[na].energy;
abondtype = ahit[na].bondtype;
agcat = ((abondtype >> 4) + abondtype) & 0xf;
/* GC content */
s = apos1;
aend2 = apos2 + astem;
nbase = (int)(aend2 - apos1) + 1;
igc = 0;
while (s <= aend2)
{ k = *s++;
if (k >= Cytosine) if (k <= Guanine) igc++; }
gcv = 10.0*(double)igc/(double)nbase;
if (gcv < 1.0)
{ if (gcv < 0.55) continue;
ea -= 0.5; }
if (nbase > 60)
{ if (gcv > 6.0) ea -= 2.0*(gcv - 6.0); }
else
{ if (gcv > 5.0) ea -= 2.0*(gcv - 5.0); }
if (gcv > 6.6)
{ ea -= 6.0;
if (gcv > 7.0) ea -= 6.0; }
/* findout if inside a coding sequence */
incds = 0;
i = -1;
while (++i < ncdsh)
if (apos1 > cdshit[i].pos1)
if (aend2 <= cdshit[i].pos2)
{ incds = 1;
ea -= 2.0;
break; }
/* if (incds) continue; */
/*
s = apos1 + nbase/2;
if (incodon(s-75,s+75) > 30.0) /@ 3.5,3.0,2.5 @/
{ incds = 1;
ea -= 2.0; }
else
incds = 0;
*/
/*
s = apos1 + nbase/2;
if (incodon(s-150,s+150) > 0.0)
{ incds = 1;
ea -= 2.0; }
else
incds = 0;
*/
/* cycle through carms that fall between astem */
nc = -1;
while (++nc < nch)
{ cpos = chit[nc].pos;
dloop = (int)(cpos - aend1);
if (dloop < 3) continue;
if (dloop > 26) continue;
cend = chit[nc].end;
tloop = (int)(apos2 - cend);
if (tloop < 5) continue;
cloop = chit[nc].loop;
cstem = chit[nc].stem;
clooppos = chit[nc].looppos;
cloopend = clooppos + cloop;
carm = chit[nc].arm;
anticodon = chit[nc].anticodon;
cbondtype = chit[nc].bondtype;
acbondtype = abondtype + cbondtype;
cgcat = ((cbondtype >> 4) + cbondtype) & 0xf;
ec = ea + chit[nc].energy;
/* astem,cstem stability (GC bond count) */
if ((abondtype & 0xf) <= 0)
if ((cbondtype & 0xf) <= 0)
{ ec -= mtGCPENALTYD;
if (((cbondtype & 0xf0) >> 4) >= 5) ec += 0.5; }
/* anticodon to astem discriminator base match */
astem8d = 0;
if (cloop == 7)
{ if (!mt_discrim[ds][anticodon][apos2[astem]])
if (astem8)
if (mt_discrim[ds][anticodon][apos2[8]]) astem8d = 1;
else ec -= 3.0;
else
if (astem <= 6)
{ if (!mt_discrim[ds][anticodon][apos2[7]])
if (astem == 5)
{ if (!mt_discrim[ds][anticodon][apos2[6]]) ec -= 3.0; }
else
ec -= 3.0; }
else
ec -= 3.0; }
/* build TV-replacement loop mttrna genes */
if (tloop <= mt_TVRLmaxlength)
{ if (!sw->tvloop) goto TVN;
/* astem termination */
/* (only need to calculate once per astem) */
if (!asteme)
{ asteme = 1;
s = aend1 - 1;
se = apos2;
while (!bp[*s][*se])
{ if (--s <= apos1)
{ eas = 0.0;
goto NOST2; }
se++; }
if (!aastemterm[s[1]][se[-1]]) eas = -0.5;
else
{ eas = 0.0;
while (se >= apos2)
{ s++;
se--;
if (aastemterm[*s][*se]) eas += 1.0; }}}
/* choose darm */
NOST2:
energy = 94.0 + ec + eas;
nd = -1;
ndi = -1;
ed = -INACTIVE;
while (++nd < ndh)
{ dpos = dhit[nd].pos;
spacer1 = (int)(dpos - aend1);
if (spacer1 != 2) continue;
dl = dhit[nd].loop;
dstem = dhit[nd].stem;
if (dstem > 4) continue;
darm = 2*dstem + dl;
spacer2 = (int)(cpos - dpos) - darm;
/* astem,darm,cstem interspacing */
if (spacer2 < 1) continue;
e = dhit[nd].energy;
if (spacer2 > 1)
{ if (spacer2 > 2) continue;
if (!stembp[*cpos][cend[-1]]) continue;
if (tloop > 12) e -= 2.0;
if ((dhit[nd].bondtype & 0xf) < 1)
if ((agcat + cgcat + 1) < (cstem + astem)) e -= 3.0; }
else
if (dl > 11)
{ if (!RI[cpos[-1]]) e -= 2.0; }
else
{ if (cpos[-1] == Cytosine) e -= 2.0; }
/* small,large dloop, dstem R motif */
if (dl < 3) e -= 2.0;
if (dl > 12) e -= 2.0;
if (!RI[*dpos]) e -= 1.0;
/* darm,tloop tertiary interaction */
k = 0;
di = ((dl >= 12)?3:((dl >= 9)?2:1));
tl = (tloop >= 14)?5:((dl >= 9)?((tloop >= 10)?4:3):3);
if (!ggstackbp[dpos[dstem+di]][cend[tl]])
{ if (tl > 3)
{ if (!ggstackbp[dpos[dstem+di]][cend[tl-1]]) e -= 1.5;
else k++; }
else
if (di > 1)
{ if (!ggstackbp[dpos[dstem+di-1]][cend[tl]]) e -= 1.5;
else k++; }
else
e -= 1.5; }
else k++;
if (stemterm[dpos[dstem-1]][dpos[darm-dstem]])
{ e -= 0.5;
if (cend[2] == dpos[dstem-2])
{ if (bp[cend[2]][dpos[darm-dstem+1]]) k++; }
else
{ if (cend[2] == dpos[darm-dstem+1])
if (bp[cend[2]][dpos[dstem-2]]) k++; }}
else
{ if (cend[2] == dpos[dstem-1])
{ if (!bp[cend[2]][dpos[darm-dstem]]) e -= 0.5;
else k++; }
else
{ if (cend[2] != dpos[darm-dstem]) e -= 0.5;
else
if (!bp[cend[2]][dpos[dstem-1]]) e -= 0.5;
else k++; }}
if (cend[1] == *dpos)
{ if (!stackbp[cend[1]][dpos[darm-1]]) e -= 0.5;
else k++; }
else
{ if (cend[1] != dpos[darm-1]) e -= 0.5;
else
if (!bp[cend[1]][*dpos]) e -= 0.5;
else k++; }
/* darm stability */
dstemmotif = wcbp[dpos[1]][dpos[darm-2]];
if (spacer2 == 2)
if ((k < 3) || (dhit[nd].bondtype > 0x200) || (!dstemmotif))
{ if (abondtype >= 0x10000) e -= 2.0;
if (dstem > 3) e -= 1.0;
e -= 0.5; }
/* darm tertiary interactions */
j = 0;
b8 = dpos[-2];
b9 = dpos[-1];
if (!bp[b8][dpos[dstem]]) e -= 1.0;
else if (wcbp[b8][dpos[dstem]]) j++;
if (!bp[b8][dpos[darm-dstem-1]]) e-= 1.0;
else if (wcbp[b8][dpos[darm-dstem-1]]) j++;
if (!wcbp[dpos[2]][dpos[darm-3]])
{ if (!gastembp[b8][dpos[dstem]]) e -= 2.0;
else if (!gastembp[b8][dpos[darm-dstem-1]]) e -= 2.0;
if (!ggstembp[dpos[2]][dpos[darm-3]]) e -= 1.0; }
else j++;
if (!bp[b9][dpos[2]])
{ if (!bp[b9][dpos[darm-3]]) e -= 1.0;
else j++; }
else j++;
/* more extensive tertiary interaction between darm,tloop */
if (dstemmotif)
{ if (k >= 3)
if (bp[dpos[2]][dpos[darm-3]])
{ if (b8 != Thymine) e += 0.5;
if (dl > 3)
if (bp[dpos[dstem+2]][cend[tl+1]]) e += 0.7;
else
if (gabp[dpos[dstem+2]][cend[tl+1]]) e += 0.5;
if (tloop >= 6)
if (spacer2 < 2)
if (dl >= 3)
{ di = (dl > 11)?2:1;
if (bp[dpos[dstem+di]][cend[tl]])
{ if (chit[nc].stem_energy > -4.8) e += 0.5;
if (wcbp[dpos[dstem+di]][cend[tl]])
if (gcv > 1.2)
if (clooppos[1] == Thymine)
if (cbondtype < 0x200)
if ((cbondtype & 0xf) > 0)
if (abondtype < 0x2000)
{ e += 1.5;
if (dl > 3)
if (wcbp[dpos[dstem+di+1]][cend[tl+1]])
e += 1.0; }}}}
if (j >= 4) e += 0.25; }
if (e > ed)
{ ed = e;
ndi = nd;
ti = k; }}
if (ndi < 0) goto TVN;
energy += ed;
dpos = dhit[ndi].pos;
dstem = dhit[ndi].stem;
dl = dhit[ndi].loop;
darm = 2*dstem + dl;
dbondtype = dhit[ndi].bondtype;
spacer2 = (int)(cpos - dpos) - darm;
spacer1 = (int)(dpos - aend1);
b8 = *aend1;
b9 = aend1[1];
/* false positive suppression */
if (dloop < 15) energy -= 2.0;
if (cstem > 5) energy -= 1.0;
if (tloop < 6) energy -= 1.0;
if (tloop > 12)
{ energy -= 1.0;
if (agcat < 6) energy -= 2.0;
if (tloop > 15) energy -= 2.5; }
if (!stackbp[*dpos][dpos[darm-1]]) energy -= 1.0;
if (dstem < 4)
if (gcv > 1.2)
if ((dbondtype & 0xf0f) == 0) energy -= 1.5;
if (b8 != Thymine)
{ if (dl < 4)
if (abondtype > 0x10000)
energy -= 1.5;
if (b8 == Adenine)
if (YI[cloopend[-2]])
energy -= 1.0; }
if (dl > 10)
{ if (tloop < 7) energy -= 2.0;
if (spacer2 > 1) energy -= 2.0;
if (dhit[ndi].stem_energy < -3.4) energy -= 2.0; }
if (gcv < 2.0)
if (dbondtype > 0x10000) energy -= 2.0;
if ((cbondtype & 0xf) < 1)
if (abondtype > 0x100)
{ if (cgcat < 4)
energy -= 1.5;
if (!wcbp[dpos[2]][dpos[darm-3]]) energy -= 1.0; }
if (b8 != Thymine)
if ((clooppos[1] != Thymine) ||
(*clooppos != Cytosine))
if (dl > 3)
if (dbondtype > 0x10000)
energy -= 1.0;
if (!RI[cend[1]])
if (b9 != Guanine) energy -= 1.0;
else energy -= 0.5;
if (b9 == Guanine)
{ if (!RI[*cend]) energy -= 1.0;
if (spacer2 != 1) energy -= 3.0;
else
{ tl = (tloop >= 14)?5:((dl >= 9)?((tloop >= 7)?4:3):3);
s = dpos + dstem;
if (!wcbp[s[1]][cend[tl]])
{ energy -= 2.5;
if (dl >= 5)
if (chit[nc].energy > 2.0)
if (wcbp[s[2]][cend[tl]])
if (wcbp[s[3]][cend[tl+1]])
energy += 6.0; }
else
if (b8 == Thymine)
if (dl >= 5)
if (chit[nc].energy > 2.0)
if (wcbp[s[2]][cend[tl+1]])
energy += 3.5; }}
else if (b9 != Adenine) energy -= 3.0;
if (b8 != Thymine)
if (b8 == Guanine)
{ if (!RI[dpos[dstem]]) energy -= 1.0;
else
if (RI[dpos[darm-dstem-1]]) energy += 2.0; }
else energy -= 1.0;
/* carm termination */
if (assymst[cend[-1]][*cpos]) energy += 1.0;
/* CTnnnAA cloop motif */
energy += CX7[*clooppos] + AX7[cloopend[-2]];
if (clooppos[1] == Cytosine) energy -= 2.0;
/* NNnnnAA cloop motif */
if (cloopend[-2] == Adenine)
if (cloopend[-1] == Adenine)
if (spacer1 == 2)
if (dbondtype < 0x1000)
{ if (abondtype < 0x100) energy += 1.0;
else
if (cbondtype < 0x100) energy += 1.0; }
/* global stem damage level */
bondtype = acbondtype + dbondtype;
i = (int)((bondtype >> 16) & 0xf);
j = (int)((bondtype >> 12) & 0xf);
k = (int)((bondtype >> 8) & 0xf);
if (k > 0)
if (i > 0)
{ k += (i + j);
if (k > 5) energy -= 1.0*(double)(k - 5); }
/* global stem stability (GC bond count) */
gcc = bondtype & 0xf;
if (gcc < 2)
{ if (ti >= 2)
{ if (cbondtype < 0x100)
if ((cbondtype & 0xf) > 0) goto NGCC1;
if (ti >= 3)
if (cgcat >= 4)
{ if ((cbondtype & 0xf) > 0) goto NGCC1;
if (cbondtype < 0x100) goto NGCC2; }}
energy -= (double)(3 - gcc);
NGCC2:
if (gcc < 1)
{ if (agcat < 5) energy -= 2.0;
if (bondtype > 0x10000) energy -= 1.5; }}
NGCC1:
/* global stability */
/* (stem stability,dloop-tloop tertiary interaction,dloop size) */
if (abondtype > 0x1000)
if (ti < 3)
{ if (chit[nc].stem_energy < -6.0)
energy -= 1.5;
if (dl > 9)
if (((dbondtype + cbondtype) & 0xf) < 1)
energy -= 1.0; }
/* tloop,dloop tertiary interaction */
/* (alternative dloop position) */
if (bondtype < 0x1000)
if (b8 == Thymine)
if (RI[b9])
if (dl > 4)
if (!bp[cend[3]][dpos[dstem+1]])
if (bp[cend[3]][dpos[dstem+2]])
energy += 0.5;
/* "near perfect" TV-loop mttRNA: */
/* darm-tloop tertiary interaction,low global stem damage, */
/* TR motif at b8-9, good astem,darm,carm interspacing */
if (ti >= 2)
if (agcat >= 6)
if (cbondtype < 0x100)
if (dbondtype < 0x100)
if (RI[b9])
if (b8 == Thymine)
if ((abondtype & 0xf) > 0)
if ((dbondtype & 0xf) > 0)
if (spacer1 == 2)
if (spacer2 == 1)
energy += 1.5;
/* find exceptions */
if (energy < dthresh)
{ if (!mtxdetect) goto TVN;
if (incds) goto TVN;
if (energy < (thresh - 7.0)) goto TVN;
if (energy < (dthresh - 7.0)) goto TVN;
if (nbase > 68) goto TVN;
if (abondtype > 0x20100) goto TVN;
if (dl > 9)
{ if (dl > 10) goto TVN;
if (dstem < 4) goto TVN;
if (dbondtype > 0x100) goto TVN; }
if (dstem > 4) goto TVN;
if (b9 != Adenine)
{ if (b9 != Guanine) goto TVN;
if (cbondtype > 0x100) goto TVN;
if (dbondtype > 0x200) goto TVN; }
if (cloop != 7) goto TVN;
if (YI[cloopend[-2]]) goto TVN;
if (b8 == Thymine)
{ if (apos2[-1] == Thymine)
if (apos2[-2] == Thymine)
if (tloop < 8)
if (tt[aend1[-1]][*apos2])
if (wcbp[dpos[2]][dpos[darm-3]])
if (((dbondtype + cbondtype) & 0xf) > 0)
energy += 3.0; }
else
if (b8 == Adenine)
{ if (apos2[-1] == Adenine)
if (apos2[-2] == Adenine)
{ if (assymat[aend1[-1]][*apos2])
if (assymat[apos2[1]][aend1[-2]]) energy += 2.0;
if (agcat >= 5)
if (cgcat >= 4)
if (dbondtype < 0x100)
if (at[aend1[-1]][*apos2])
if (at[apos2[1]][aend1[-2]])
energy += 1.0; }
if (ti >= 3)
if (cgcat >= 4)
if (agcat >= 4)
if ((cbondtype & 0xf) > 0)
if ((abondtype & 0xf) > 1)
if (dbondtype < 0x200)
if (wcbp[dpos[1]][dpos[darm-2]])
if (clooppos[1] == Thymine)
if (YI[*clooppos])
if (RI[cloopend[-2]])
if (RI[cloopend[-1]])
energy += 5.0; }
if (bondtype < 0x100)
{ if (spacer2 == 1)
if (*clooppos == Cytosine)
if (clooppos[1] == Thymine)
if (cloopend[-2] == Adenine)
if (cloopend[-1] == Adenine)
energy += 2.0; }
else
{ if (spacer2 == 1)
{ if (b8 == Thymine)
if (dl > 3)
if (dbondtype < 0x200)
{ if (cbondtype < 0x100)
{ if (!bp[dpos[dstem+1]][cend[3]])
if (bp[dpos[dstem+1]][cend[4]])
energy += 2.0;
if (dbondtype < 0x100)
if (abondtype < 0x20000)
if (ti >= 2)
if (dstem >= 3)
if (tloop < 13)
if ((cbondtype & 0xf) > 0)
energy += 4.0; }}
else
if (dstem > 3)
if (dbondtype < 0x300)
{ if (bondtype < 0x10000)
if (ti >= 3)
if ((acbondtype & 0xf) > 0)
if (wcbp[dpos[2]][dpos[darm-3]])
energy += 4.0; }
if (tloop < 8)
{ if (dbondtype < 0x200)
{ if (cbondtype < 0x100)
if (ti >= 2)
{
if (wcbp[dpos[dstem+1]][cend[3]])
{
if (b8 == Thymine)
if (abondtype < 0x3000)
energy += 5.0;
if (agcat >= 5)
if (gcv > 1.2)
if (RI[cloopend[-1]])
energy += 7.0;
}
if (dbondtype < 0x100)
if (agcat >= 6)
if (YI[*clooppos])
if (clooppos[1] == Thymine)
if (RI[cloopend[-2]])
if (RI[cloopend[-1]])
energy += 2.0;
}
if (cbondtype < 0x300)
if (ti >= 3)
if (abondtype < 0x2000)
if ((dbondtype & 0xf) > 0)
if ((acbondtype & 0xf) > 0)
if (ahit[na].energy >= -7.0)
if (dstem >= 4)
energy += 3.0; }
if (dbondtype < 0x300)
if (cgcat >= 4)
if (abondtype < 0x2000)
if (ahit[na].energy >= -7.0)
if (cbondtype < 0x10000)
if ((cbondtype & 0xf) > 0)
if (cstem < 6)
if (ti >= 3)
energy += 4.0; }}
if (tloop > 8)
if (agcat >= 6)
if (cbondtype < 0x100)
if ((cbondtype & 0xf) > 0)
if (b8 == Thymine)
if (wcbp[dpos[dstem+1]][cend[3]])
if (wcbp[dpos[1]][dpos[darm-2]])
energy += 7.0; }
if (dbondtype < 0x100)
if (cgcat >= 4)
if (agcat >= 5)
if (wcbp[dpos[1]][dpos[darm-2]])
if ((cbondtype & 0xf) > 0)
if ((abondtype & 0xf) > 0)
if ((dbondtype & 0xf) > 0)
energy += 0.5;
if (cbondtype < 0x100)
if (dbondtype < 0x200)
if (agcat >= 5)
if (b8 == Thymine)
if (tloop < 8)
if (wcbp[dpos[1]][dpos[darm-2]])
if (wcbp[dpos[2]][dpos[darm-3]])
if ((cbondtype & 0xf) > 0)
if ((abondtype & 0xf) > 0)
if ((dbondtype & 0xf) > 0)
if (clooppos[1] == Thymine)
if (YI[*clooppos])
if (RI[cloopend[-2]])
energy += 3.0;
if (energy < dthresh) goto TVN;
energy -= (0.9*(energy - dthresh) + 5.0); }
/* remember fully formed TV-loop replacement mttRNA gene */
/* if threshold reached */
if (energy < thresh) goto TVN;
te.energy = energy;
thresh = energy;
te.ps = apos1;
te.dstem = dstem;
te.dloop = dl;
te.spacer1 = spacer1;
te.spacer2 = spacer2;
te.cstem = cstem;
te.cloop = cloop;
k = astem + spacer1 + darm + spacer2;
te.anticodon = k + cstem + 2;
te.nintron = 0;
te.intron = 0;
te.var = 0;
te.varbp = 0;
te.tstem = 0;
te.tloop = tloop;
te.nbase = k + carm + tloop;
tastem = astem;
tastem8 = astem8;
tastem8d = astem8d;
/* build D-replacement loop mttrna genes */
TVN:
if (tloop < 10) continue; }
if (dloop > mt_DRLmaxlength) goto DN;
if (gcv < 1.2) goto DN;
energy = 91.0 + ec;
/* CCnnnAA cloop */
if (clooppos[1] == Cytosine)
{ if (*clooppos != Cytosine) goto DN;
if (cloopend[-2] != Adenine) goto DN;
if (cloopend[-1] != Adenine) goto DN;
energy -= 1.0; }
/* choose tarm */
nt = -1;
nti = -1;
et = -INACTIVE;
while (++nt < nth)
{ tl = thit[nt].loop;
if (tl > 11) continue;
if (thit[nt].end != apos2) continue;
tpos = thit[nt].pos;
tstem = thit[nt].stem;
/* var loop (3-7 bases long) */
var = (int)(tpos - cend);
if (var < 3) continue;
e = thit[nt].energy;
if (var > 5)
{ if (var > 7) continue;
if (tl < 7) continue;
e -= 1.0;
if ((dloop < 10) || (tstem < 4))
e -= 2.0*(double)(var - 5); }
/* tloop RA or RG motif */
s = tpos + tstem;
k = 0;
n = 0;
i = 0;
while ((j = tloopa[tl][i++]) >= 0)
if (s[j] == Adenine)
{ k = 1;
if (dloop >= 3)
if (tl > 3)
{ b57 = s[j-1];
if (RI[b57] || (tl < 5))
{ if (bp[b57][aend1[0]])
{ e += 1.5;
n = 1;
break; }
if (bp[b57][aend1[1]])
{ e += 1.5;
n = 1;
break; }
if (dloop > 10)
if (bp[b57][aend1[2]])
{ e += 1.5;
n = 1;
break; }}}}
if (!k)
{ i = 0;
while ((j = tloopa[tl][i++]) >= 0)
if (s[j] == Guanine)
if (RI[s[j-1]])
{ k = 1;
break; }
if ( j < 0) e -= ((tl > 5)?2.0:1.0); }
/* tertiary interaction between tloop and start of dloop */
ti = (tl > 5)?1:((dloop > 5)?1:0);
di = (dloop > 5)?2:1;
if (stackbp[aend1[di]][s[ti]]) e += 1.0;
/* tloop GTTC motif */
i = (s[-1] == Guanine)?1:0;
if (tl >= 5)
{ ti = i + TI[*s] + TI[s[1]] + CI[s[2]];
if (n)
if (!i)
if (TI[*s])
if (TI[s[1]])
if (AI[s[2]])
if (tl >= 7)
ti++;
if ((i > 0) || (ti >= 3)) e += (double)ti; }
else
{ ti = i + TI[*s] + TI[s[1]];
if ((i > 0) || (ti >= 2)) e += (double)ti; }
if (e > et)
{ et = e;
nti = nt;
tc = k; }}
if (nti < 0) goto DN;
energy += et;
tpos = thit[nti].pos;
tstem = thit[nti].stem;
tl = thit[nti].loop;
tbondtype = thit[nti].bondtype;
var = (int)(tpos - cend);
/* tertiary interaction between b48(=tpos[-1]) and dloop */
b48 = tpos[-1];
if (dloop <= 7)
{ if (YI[b48]) tc++;
else energy -= 1.0; }
else
{ i = 0;
while ((j = dloopi[dloop][i++]) >= 0)
if (assymagbp[b48][aend1[j]])
{ tc++;
break; }
if (j < 0) energy -= 1.0; }
/* large dloop, large tloop */
if (dloop > 7)
{ if (tl >= 6)
if (tc < 2)
energy -= 2.0;
if (tstem < 3)
energy -= 1.0; }
/* carm termination */
s = cpos - 1;
se = cend;
if (cstem > 5)
{ s++;
se--; }
if (!stackbp[*s][*se]) energy -= 1.0;
se = cpos - 3;
if (!bp[cend[-1]][*cpos])
{ if (assymst[cend[-1]][*cpos])
{ if (dloop < 5) se++;
energy += 1.5; }
else if (dloop < 13) se++; }
else
{ if (cstem > 5) { if (dloop < 13) se++; }
else if (dloop < 5) se++; }
/* tertiary interaction between tloop and dloop near carm */
s = tpos + tstem;
if (tl >= 5)
{ ti = (tl >= 10)?4:((tl >= 7)?3:2);
b57 = s[ti];
if (!gabp[*se][b57]) energy -= 2.0;
else
{ k = (var > 3)?2:((var > 1)?1:0);
if (bp[cend[k]][b57]) energy += 1.0; }}
/* R motif at end of tstem */
if (!RI[s[-1]]) energy -= 2.0;
/* large tloop */
if (tl > 9)
if (tbondtype > 0x200) energy -= 2.0;
/* dloop,var,tloop T repeat motif */
/* present in some nematode D-loop replacement tRNA-Ser genes */
if (dloop >= 4)
{ k = 1;
se = aend1;
while (se < cpos) if (*se++ == Thymine) k++;
if (k >= dloop)
{ if (var >= 3)
{ se = cend;
while (se < tpos) if (*se++ == Thymine) k++;
if (k >= (var + dloop))
{ energy += 3.0;
se = s + ((tl > 5)?5:tl);
while (s < se) if (*s++ != Thymine) break;
if (s >= se) energy += 5.5; }}}}
/* astem stability */
if (ea < -6.1)
if (tl > 4)
{ if (*s == Thymine)
if (s[-1] == Guanine)
if (s[1] == Thymine)
goto NASI;
if (ea > -8.3)
if (*clooppos == Cytosine)
if (clooppos[1] == Thymine)
if (cloopend[-2] == Adenine)
if (cloopend[-1] == Adenine)
goto NASI;
energy -= 3.0; }
NASI:
/* cstem stability (GC bond count) */
bondtype = acbondtype + tbondtype;
if ((cbondtype & 0xf) < 1)
if ((bondtype & 0xf) < 3) energy -= 1.0;
/* cloop CTnnnAA motif */
if (bondtype >= 0x400)
energy += CX[*clooppos] + TX[clooppos[1]] +
AXX[cloopend[-1]] + AXX37[cloopend[-2]];
else
energy += CX[*clooppos] + TX[clooppos[1]] +
AX[cloopend[-1]] + AX37[cloopend[-2]];
/* large dloop */
if (dloop >= 9)
{ k = tloop - dloop - 4;
if (k < 0)
if (bondtype >= 0x1000) energy += (double)k;
if (dloop >= 12)
{ if (dloop >= 14) energy -= 2.0;
else
if (tstem < 6) energy -= ((dloop >= 13)?2.0:1.0); }}
/* small dloop, small tarm */
if (dloop <= 10)
if (tstem < 3)
if (ea > -2.6)
if (tl <= 7)
if (cgcat >= 4)
if (gc[*tpos][apos2[-1]])
if (gc[tpos[1]][apos2[-2]])
if (gcv > 1.2)
if ((abondtype & 0xf) > 0)
if ((cbondtype & 0xf) > 0)
energy += (4.5 + (mtBONDSTAB - 0.5)*(double)(5 - tstem));
/* global stem damage level */
i = (int)((bondtype >> 16) & 0xf);
j = (int)((bondtype >> 12) & 0xf) + i;
k = (int)((bondtype >> 8) & 0xf);
if (tstem > 3)
{ if ((k > 0) || (tl > 9))
if ((j > 0) || (k > 5))
{ n = j + k;
if ((s[-1] != Guanine) || (*s != Thymine) ||
(s[1] != Thymine) || (tstem < 5))
if (n > 4) energy -= 2.0*(double)(n - 4); }}
else
{ n = j + k;
if (n > 3) energy -= 2.0*(double)(n - 3); }
/* long tstem with tloop GTT motif */
if (s[-1] == Guanine)
if (*s == Thymine)
if (s[1] == Thymine)
if (tstem >= 6)
if (tbondtype < 0x100)
energy += 1.5;
/* find exceptions */
if (energy < tthresh)
{ if (!mtxdetect) goto DN;
if (incds) goto DN;
if (energy < (thresh - 13.5)) goto DN;
if (energy < (tthresh - 13.5)) goto DN;
if (k > 1)
{ if (i > 2) goto DN;
if (k > 4)
if (i > 1) goto DN; }
if (nbase > 70) goto DN;
if (var > 4)
{ if (var > 5) goto DN;
if (var > tl) goto DN; }
if (tstem < 4)
if ((agcat + cgcat + 2) < (astem + cstem))
goto DN;
if (tl > 9) goto DN;
if (dloop > 13) goto DN;
if (!YI[*clooppos]) goto DN;
if ((abondtype & 0xf) < 2)
{ if ((abondtype & 0xf) < 1) goto DN;
if (cbondtype > 0x200)
if (tbondtype > 0x100)
if (abondtype > 0x200)
goto DN; }
if ((tbondtype & 0xf) < 1)
{ if ((acbondtype & 0xf) < 1) goto DN;
if (acbondtype > 0x200) goto DN; }
if ((dloop + 19) < tloop) goto DN;
if (gcv > 5.5) goto DN;
tgcat = ((tbondtype >> 4) + tbondtype) & 0xf;
if ((tgcat + 2) < tstem) goto DN;
if (cloop != 7) goto DN;
if (bp[*cpos][cend[-1]])
if (bp[cpos[-1]][*cend])
if (bp[cpos[-2]][cend[1]])
energy += 2.0;
if (bondtype < 0x20000)
if (thit[nti].stem_energy > -4.6)
if (tstem >= 4)
if ((tstem >= 5) || (s[-1] == Guanine))
if (stackbp[cpos[1]][cend[-2]])
if (stackbp[*cpos][cend[-1]])
if (stackbp[cpos[-1]][*cend])
{ energy += 1.5;
if (s[-1] == Guanine)
if (*s == Thymine)
if (s[1] == Thymine)
energy += 1.0;
if (agcat >= 6) energy += 0.5; }
if (tc > 0)
if (tstem >= 5)
if (var < 6)
if (var > 2)
{ if (acbondtype < 0x100) energy += 5.0;
else
if ((abondtype + tbondtype) < 0x100)
energy += 3.0;
else
if (cloopend[-2] == Thymine)
if (cloopend[-1] == Thymine)
if (dloop > 7)
if (tbondtype < 0x100)
if (!tt[*tpos][apos2[-1]])
if ((agcat+cgcat) >= 10)
energy += 13.5; }
if (s[-1] == Guanine)
if (*s == Thymine)
if (s[1] == Thymine)
if ((tstem >= 5) || (s[2] == Cytosine))
{ energy += 1.5;
if (tstem >= 5)
if (tbondtype < 0x1000)
if (s[2] == Cytosine)
{ if (abondtype < 0x10000)
{ if (*clooppos == Cytosine)
if (clooppos[1] == Thymine)
if (cloopend[-2] == Adenine)
if (cloopend[-1] == Adenine)
energy += 3.0;
if (tbondtype < 0x200)
if (bondtype < 0x10000)
if (tl == 7)
if (s[4] == Adenine)
energy += 4.0; }}
else
if (tbondtype < 0x200)
if ((tbondtype & 0xf) >= 2)
if (*clooppos == Cytosine)
if (clooppos[1] == Thymine)
if (cloopend[-2] == Adenine)
if (cloopend[-1] == Adenine)
energy += 1.0; }
if (tstem >= 4)
if (tbondtype < 0x100)
if (cbondtype < 0x200)
if (agcat >= 5) energy += 1.5;
if (energy > tthresh) energy = tthresh;
if (ea > -1.8) energy += 3.0;
else
if (abondtype < 0x60) energy += 1.5;
else
if (acbondtype < 0x200) energy += 0.75;
if (*clooppos == Cytosine)
if (cloopend[-2] == Adenine)
if (cloopend[-1] == Adenine)
{ if (tstem >= 5)
if (tbondtype < 0x100)
if (clooppos[1] == Thymine)
{ energy += 3.0;
if (tstem >= 6) energy += 1.0; }
else
if (clooppos[1] == Cytosine)
energy += 1.0;
if (tc >= 2)
if (clooppos[1] == Thymine)
if (bondtype < 0x1000)
if (tstem >= 4)
if (var < 6)
if (var > 2)
energy += 3.0; }
if (cbondtype < 0x100)
if (agcat >= 5)
if (tc > 0)
if (clooppos[1] == Thymine)
if (YI[*clooppos])
if (RI[cloopend[-2]])
if (RI[cloopend[-1]])
if (tbondtype < 0x100)
energy += 4.0;
else
if (agcat >= 6)
if ((tgcat + 1) >= tstem)
if (tstem >= 4)
energy += 4.0;
if (bondtype < 0x1000)
{ energy += 0.5;
if (bondtype < 0x200) energy += 0.75; }
if (energy < tthresh) goto DN;
energy -= (3.0 + 0.9*(energy - tthresh)); }
/* mammalian cloop motif constraint */
if (ds == MAMMAL_MT)
{ s1 = clooppos;
s2 = s1 + cloop;
r = *s1++;
while (s1 < s2) r = (r << 4) + *s1++;
if (r != clmotif[0])
if (r != clmotif[1])
if (r != clmotif[2])
energy -= 5.0; }
/* remember fully formed D-loop replacement mttRNA gene */
/* if threshold reached */
if (energy < thresh) goto DN;
te.energy = energy;
thresh = energy;
te.ps = apos1;
te.spacer1 = 0;
te.spacer2 = 0;
te.dstem = 0;
te.dloop = dloop;
te.cstem = cstem;
te.cloop = cloop;
te.anticodon = astem + dloop + cstem + 2;
te.nintron = 0;
te.intron = 0;
te.var = var;
te.varbp = 0;
te.tstem = tstem;
te.tloop = tl;
te.nbase = astem + dloop + carm + var +
2*tstem + tl;
tastem = astem;
tastem8 = astem8;
tastem8d = astem8d;
/* build fully formed cloverleaf mttRNA genes */
DN:
if (dloop < 10) continue;
/* choose tarm */
nt = -1;
nti = -1;
et = -INACTIVE;
while (++nt < nth)
{ tend = thit[nt].end;
if (tend != apos2) continue;
e = thit[nt].energy;
tpos = thit[nt].pos;
tstem = thit[nt].stem;
/* GT motif on tloop */
s = tpos + tstem;
if (*s == Thymine)
if (s[-1] == Guanine)
if (tstem >= 5)
if (!stackbp[*tpos][tend[-1]])
{ e += 0.5;
if (!bp[tpos[1]][tend[-2]]) e += 0.5; }
/* large var loop */
var = (int)(tpos - cend);
if (var > 5)
{ ev = (double)(var - 5);
if (tstem < 5) e -= 3.0*ev;
else e -= (0.5 + 0.5*ev);
/* allow large var loop if tarm looks nuclear */
/* (GTTC motif, very large var loop base-pairing) */
if (var > 9)
{ if ((thit[nt].bondtype & 0xf) < 1) e -= 1.0;
e -= (0.25*(double)(var - 8));
if (*s == Thymine)
if (s[-1] == Guanine)
if (s[1] == Thymine)
if (s[2] == Cytosine)
e += 4.0;
if (var > 17)
{ if (var > 25) continue;
e += 0.5*vloop_stability(cend,var,&varbp); }}}
/* small var loop */
if (var < 3)
{ if (tstem > 5)
if (s[-1] != Guanine)
e -= 0.5;
if (var < 2)
{ if (var < 1)
{ if (var < 0) continue;
if (tstem < 4)
if (thit[nt].stem_energy < -4.0)
continue; }
e -= 3.0; }}
if (e > et)
{ et = e;
nti = nt; }}
if (nti < 0) continue;
tpos = thit[nti].pos;
tstem = thit[nti].stem;
tl = thit[nti].loop;
tarm = 2*tstem + tl;
var = (int)(tpos - cend);
b48 = tpos[-1];
tbondtype = thit[nti].bondtype;
bondtype = acbondtype + tbondtype;
ti = (int)(((bondtype >> 16) & 0xf) + ((bondtype >> 12) & 0xf) +
((bondtype >> 8) & 0xf));
/* choose darm */
nd = -1;
ndi = -1;
ed = -INACTIVE;
while (++nd < ndh)
{ dl = dhit[nd].loop;
dstem = dhit[nd].stem;
darm = 2*dstem + dl;
dpos = dhit[nd].pos;
e = dhit[nd].energy;
/* spacing between astem,darm,carm */
spacer1 = (int)(dpos - aend1);
spacer2 = (int)(cpos - dpos) - darm;
if (spacer1 < 2)
{ if (spacer1 < 1) continue;
if (dstem < 3) continue;
if (dl > 12) e -= 2.0;
if (astem < 7) e -= 1.0;
if (spacer2 != 2)
{ if (spacer2 < 1) continue;
if (spacer2 > 2) continue;
if ((abondtype & 0xf) < 1)
if ((dhit[nd].bondtype & 0xf) < 1)
e -= 0.5;
if (var > 7) e -= 1.0;
if (dl > 12) e -= 1.0;
if (cloop != 7) e-= 2.0;
if (cstem < 6) e -= 3.6;
else e -= 0.5; }
else
{ if (cstem > 5) continue;
s = cpos;
se = cend-1;
while (!bp[*s][*se])
{ s++;
se--; }
if (!stemterm[s[-1]][se[1]]) e -= 0.5;
e -= 0.8; }}
else
{ if (spacer1 > 2)
{ if (spacer1 > 3) continue;
if (dstem > 4) continue;
if (dstem < 3) continue;
if (tl > 15) continue;
if (astem < 7) e -= 1.0;
if (ti > 4) e -= 1.0;
if (cloop != 7) e-= 2.0;
if (tbondtype > 0x2000)
if (!RI[tpos[tstem-1]]) e -= 2.0;
e -= 1.0;
if (spacer2 != 1) e -= 0.5;
else
if (dhit[nd].bondtype < 0x100)
if (var >= 3)
if (var <= 5)
if (tstem >= 3)
{ e += 1.0;
if (agcat >= 5)
if (wcbp[*aend1][*apos2])
if (!bp[aend1[-1]][*apos2])
if (bp[b48][dpos[dstem+1]])
e += 0.5; }
}
if (spacer2 > 1)
{ if (spacer2 > 2) continue;
if (astem < 7)
if (spacer1 == 2)
e -= 1.0;
if (cloop != 7) e -= 2.0;
if (ea < -5.8) e -= 2.0;
e -= 2.5;
if (bp[b48][dpos[dstem+1]])
{ if (dhit[nd].bondtype < 0x1000)
if (wcbp[dpos[1]][dpos[darm-2]])
if (wcbp[dpos[2]][dpos[darm-3]])
if (var < 6)
if (dl > 3)
e += 2.0; }
else e -= 1.0;
}
else
if (spacer2 < 1)
{ if (spacer2 < 0) continue;
if (var > 6) continue;
if (dstem > 4) continue;
if (dhit[nd].stem_energy < -4.3) continue;
if (astem < 7)
if (spacer1 == 2)
e -= 1.0;
if (cloop != 7) e-= 2.0;
e -= mtBONDSTAB; }
if (cstem > 5)
if ((!gt[*cpos][cend[-1]]) || astem8) e-= mtBONDSTAB; }
/* very large or very small dloop */
if (dl < 3) e -= 2.0;
if (dl > 11)
{ if (dl > 14) e -= 2.0;
else
if (dl > 13)
{ if (dhit[nd].bondtype >= 0x100) e -= 2.0;
else e -= 1.0; }
else
if (dl > 12)
{ if (dhit[nd].bondtype >= 0x1000) e -= 2.0;
else e -= 1.0; }
else
if (dhit[nd].bondtype >= 0x10000) e -= 2.0; }
/* tertiary interactions in darm */
b8 = dpos[-2];
b9 = dpos[-1];
if (dl > 2)
{ if (dl > 5)
if (!stackbp[dpos[dstem+1]][b48]) e -= 1.0;
if (!stackbp[b8][dpos[dstem]]) e-= 0.25;
if (!stackbp[b8][dpos[dstem+dl-1]]) e -= 0.25; }
if (!bp[b9][dpos[2]])
if (!bp[b9][dpos[darm-3]])
e -= 1.0;
/* TR motif at b8-9 */
if (RI[b9])
{ if (b8 == Thymine)
if (spacer1 == 2)
if (ti < 6)
if (((bondtype & 0xf) > 2) || (bondtype < 0x1000) ||
((tbondtype < 0x100) && (tstem > 3)))
if ((cbondtype & 0xf) < 5)
if (stembp[dpos[1]][dpos[darm-2]])
if (var < 6)
if (var > 2) e += 1.5;
else
if (tstem > 3)
if (cloopend[-2] == Adenine)
e += 1.5; }
else
{ e -= 1.0;
if (b9 == Thymine)
if (spacer1 == 2) e -= 2.0; }
if (e > ed)
{ ed = e;
ndi = nd; }}
if (ndi < 0) continue;
energy = 100.0 + ec + ed + et;
dl = dhit[ndi].loop;
dstem = dhit[ndi].stem;
darm = 2*dstem + dl;
dpos = dhit[ndi].pos;
dbondtype = dhit[ndi].bondtype;
spacer1 = (int)(dpos - aend1);
spacer2 = (int)(cpos - dpos) - darm;
b8 = dpos[-2];
/* tertiary structure interaction between tloop and dloop */
if (tl >= 3)
if (dl >= 4)
{ di = (dl < 7)?(darm-dstem-2):(darm-dstem-3);
ti = (tl < 9)?(tstem+2):((tl < 13)?(tstem+3):(tstem+5));
if (ggbp[dpos[di]][tpos[ti]])
if (ggbp[dpos[di-1]][tpos[ti-1]])
{ energy += 2.0;
if (spacer1 != 2)
if (spacer2 != 2)
if (dstem < 4)
if (tl > 7)
if (bp[dpos[di+1]][tpos[ti+1]])
energy += 4.0;
if (ea > -2.5)
if (wcbp[dpos[1]][dpos[darm-2]])
if (wcbp[dpos[2]][dpos[darm-3]])
energy += 3.0; }
if (tl > 10)
if (dl > 10)
energy -= 1.0; }
else
if (dl == 3)
if (wcbp[dpos[dstem+1]][b48]) energy += 1.0;
/* small darm and tarm */
if (tloop <= 18)
if (tarm <= 13)
if (dl <= 8)
if (spacer1 == 2)
if (spacer2 == 1)
if (abondtype < 0x1000)
if (tbondtype < 0x100)
if (dbondtype < 0x200)
{ et = (mtBONDSTAB - 0.5)*(double)(5 - tstem) +
0.1*(double)(7-tl);
ed = mtBONDSTAB*(double)(4 - dstem);
energy += (0.8*(et + ed)); }
/* GTTC motif on tloop */
s = tpos + tstem;
if (tl < 5)
if (tl < 2) energy += G[s[-1]];
else
{ et = (G[s[-1]] + T[*s] + T[s[1]]);
if (tl > 3)
if (bp[*s][s[tl-1]])
{ e = (G[*s] + T[s[1]] + T[s[2]]);
if (e > et) et = e; }
if (tstem < 5)
{ e = (G[s[-2]] + T[s[-1]] + T[*s] + C[s[1]]);
if (e > et) et = e; }
energy += et; }
else energy += (G[s[-1]] + T[*s] + T[s[1]] + C[s[2]]);
/* long astem */
if (astem8)
if (bp[apos1[0]][apos2[6]])
if (bp[apos1[1]][apos2[5]])
if (bp[apos1[2]][apos2[4]])
if (bp[apos1[3]][apos2[3]])
energy += hbem[apos1[-1]][apos2[7]];
/* false positive supression */
if (!RI[cend[0]]) energy -= 1.0;
if (!RI[cpos[-1]]) energy -= 1.0;
if (tarm < (var + 3)) energy -= 2.0;
if (gcv < 1.5)
if (dbondtype > 0x10000) energy -= 2.0;
if (tarm > 27)
{ energy -= 1.0;
if (spacer2 != 1) energy -= 1.0; }
if (dstem < 3)
{ if (var > 5) energy -= 1.0;
if (tloop > (dloop + 8)) energy -= 0.5; }
if (b8 != Thymine)
if (dl > 3)
if (dbondtype > 0x100)
if ((b8 == Cytosine) ||
(dbondtype > 0x10000))
if (*clooppos != Cytosine)
if (!wcbp[dpos[dstem+1]][b48])
energy -= 1.0;
/* high GC false positive suppression */
if (gcv >= 5.1)
{ if ((abondtype & 0xf) >= 4)
{ s1 = apos1;
s2 = apos2 + astem;
n = 0;
while (--s2 >= apos2)
if (gc[*s1++][*s2])
{ if (++n >= 4)
{ energy -= 2.0;
break; }}
else n = 0; }
if ((dbondtype & 0xf) >= 4) energy -= 3.0;
if ((cbondtype & 0xf) >= 5) energy -= 3.5;
if ((tbondtype & 0xf) >= tstem) energy -= 4.0; }
/* global stem damage level */
tc = tstem + dstem;
dtbondtype = dbondtype + tbondtype;
mabondtype = dtbondtype + cbondtype;
bondtype = acbondtype + dtbondtype;
if (bondtype < 0x100) energy += 0.5;
if ((dtbondtype & 0xf) < 1)
{ energy -= 1.0;
if (tc >= 10) energy -= 2.0;
if ((bondtype & 0xf) < 3)
if (nbase > 75) energy -= 1.0; }
i = (int)((bondtype >> 16) & 0xf);
j = (int)((bondtype >> 12) & 0xf) + i;
k = (int)((bondtype >> 8) & 0xf) + j;
ti = (tc > 6)?5:((tc > 5)?4:3);
if (k > ti)
{ ev = (double)(k - ti);
energy -= 0.5*ev;
if (cbondtype > 0x10000)
if (tstem < 5)
energy -= ev;
if (i > 0)
if (k > 8)
energy -= 1.5*(double)(k - 8); }
/* low GC false positive supression */
if (gcv < 3.5)
if ((bondtype & 0xf) < 2)
{ if ((bondtype & 0xf) < 1) energy -= 1.0;
if (dl > 3)
if (var > 2)
if (!wcbp[dpos[dstem+1]][b48]) energy -= 1.0; }
/* small variable loop */
if (var < 3)
{ if (dloop > 18)
{ if (dloop > (tloop + 2)) energy -= 1.0;
if (tloop > 20)
if ((((dtbondtype >> 4) + dtbondtype) & 0xf) < 6)
energy -= 2.0; }
if (astem < 7)
{ energy -= 1.0;
if (agcat >= 5)
if (bondtype < 0x300)
if (gcv > 1.2)
if (gcv < 5.0)
energy += 2.0; }}
else
/* NNNNNAA cloop */
if (cloopend[-2] == Adenine)
if (cloopend[-1] == Adenine)
if (spacer1 > 1)
if ((dbondtype < 0x2000) || (dloop > mt_DRLmaxlength))
{ if (abondtype < 0x100) energy += 1.0;
else
if (cbondtype < 0x100) energy += 1.0;
else
if (tstem >= 5)
if (tbondtype < 0x100)
{ energy += 1.0;
if (*clooppos == Cytosine)
if (clooppos[1] == Thymine)
if (dbondtype < 0x100)
energy += 0.5;
if (cgcat >= 3)
if ((tbondtype & 0xf) > 0)
if (ggbp[dpos[dstem+1]][b48])
if (wcbp[dpos[1]][dpos[darm-2]])
if (tl < 10)
if (spacer1 == 2)
if (spacer2 == 1)
if (dl > 2)
if (var >= 2)
if (var < 6)
{ if (agcat >= 6) energy += 3.0;
else
if (agcat >= 5)
if (cgcat >= 4)
if (dbondtype < 0x100)
if (*s == Thymine)
if (s[-1] == Guanine)
if (s[1] == Thymine)
energy += 3.0; }}}
/* large tloop */
if (tl > 12)
{ if (tbondtype > 0x10000) energy -= 2.0;
if (agcat < 5)
if (spacer1 != 2)
if (spacer2 != 1)
energy -= 1.0; }
/* find exceptions */
if (energy < dtthresh)
{ if (!mtxdetect) continue;
if (incds) continue;
if (energy < (thresh - 12.0)) continue;
if (energy < (dtthresh - 12.0)) continue;
if (nbase > 75) continue;
if (dstem > 4) continue;
if (dstem < 3) continue;
if (astem < 7)
if (acbondtype > 0x21000)
continue;
if (var > 5)
{ if (var > 6) continue;
if (tarm < 12) continue; }
if (gcv <= 1.2)
{ if (gcv < 0.9) continue;
if ((mabondtype & 0xf) < 1) continue; }
if (tl > 9)
{ if (tl > 13) continue;
if (!wcbp[dpos[1]][dpos[darm-2]])
continue; }
if (dl > 7)
{ if (bondtype > 0x20000)
if (dloop > (tloop + 4)) continue;
if (dl > 10)
{ if (dl > 12)
if (abondtype > 0x1000)
continue;
if (tbondtype > 0x200) continue;
if (tt[*tpos][apos2[-1]]) continue;
if (var > 5) continue;
if (dloop > (tloop + 8))
if (bondtype > 0x10000) continue;
if (astem < 7) continue; }}
if (RI[clooppos[1]]) continue;
b9 = dpos[-1];
if (cstem >= 6)
{ if (cbondtype > 0x200) continue;
if (var < 3) continue;
if (YI[b9]) continue; }
if (cloop != 7) continue;
if (ds == MAMMAL_MT) continue;
if (mabondtype < 0x400)
{ if ((b8 == Thymine) || (mabondtype < 0x300))
if (ea < -5.45)
if (chit[nc].stem_energy > -3.2)
if (dbondtype < 0x200)
if (spacer1 > 1)
if ((spacer2 == 1) || (mabondtype < 0x100))
if ((spacer1 < 3) || (tstem > 3) ||
(tbondtype < 0x100))
if ((spacer1 < 3) ||
((var > 2) && (var < 6) && (tbondtype < 0x2000) &&
(tl < 10)))
if (dstem < 5)
if (var >= 2)
if (dl > 2)
if (tl < 15)
if ((b8 != Cytosine) ||
(*clooppos == Cytosine))
if (RI[b9])
if (*clooppos != Adenine)
if (clooppos[1] == Thymine)
if (RI[cloopend[-2]])
{ s1 = apos1;
s2 = apos2 + astem;
n = 0;
while (--s2 >= apos2)
if (wcbp[*s1++][*s2])
{ if (++n >= 3) break; }
else n = 0;
if (n >= 3)
{ energy += 3.0;
if ((abondtype & 0xf) > 0) energy += 2.0;
if (bp[dpos[dstem+1]][b48])
if (wcbp[dpos[1]][dpos[darm-2]])
if (var <= 5)
energy += 1.0; }
if (dtbondtype < 0x200)
if (agcat < 2)
if (wcbp[dpos[dstem+1]][b48])
if (wcbp[dpos[1]][dpos[darm-2]])
if (wcbp[dpos[2]][dpos[darm-3]])
if (gcv > 1.2)
if (var <= 5)
if (tstem >= 3)
if (dstem >= 3)
if (tl > 3)
if (tl < 9)
if (dl < 9)
if (spacer1 == 2)
energy += 10.0; }
if ((tbondtype & 0xf) > 0)
if (mabondtype < 0x300)
{ if (mabondtype < 0x100)
{ if ((spacer1 < 3) || (tstem > 2))
if (var > 0)
if (YI[*clooppos])
if ((spacer2 > 0) || (clooppos[1] == Thymine))
energy += 2.5; }
else
if ((dbondtype & 0xf) > 0)
if (b9 != Cytosine)
if (var <= 7)
if (spacer2 == 1)
if (tarm < 22)
if (gcv > 1.2)
if (dstem >= 4)
{ if (tstem >= 5)
energy += 5.0;
else
if (tstem >= 3)
if (tbondtype < 0x100)
energy += 1.0; }
else
if (tstem >= 5)
energy += 1.0; }
else
if ((dbondtype & 0xf) > 0)
{ if (tstem >= 5)
if (s[-1] == Guanine)
if (*s == Thymine)
if (s[1] == Thymine)
if (*clooppos == Cytosine)
if (clooppos[1] == Thymine)
if (cloopend[-2] == Adenine)
if (cloopend[-1] == Adenine)
energy += 1.0;
if (bondtype < 0x1000)
if (cbondtype < 0x100)
energy += 1.0; }}
if (tstem >= 5)
if (*clooppos == Cytosine)
{
if (dl > 3)
if (dtbondtype < 0x200)
if ((tbondtype & 0xf) > 0)
if (clooppos[1] == Thymine)
{
if (clooppos[2] == Thymine)
if (clooppos[3] == Adenine)
if (clooppos[4] == Cytosine)
if (clooppos[5] == Adenine)
if (cloop == 7)
energy += 0.5;
if (cgcat >= 4)
if (wcbp[dpos[1]][dpos[darm-2]])
if (bp[dpos[dstem+1]][b48])
if (tl < 10)
if (var < 6)
if (spacer1 == 2)
if (spacer2 == 1)
if (dstem >= 3)
energy += 3.0;
}
if (clooppos[1] == Cytosine)
if (clooppos[2] == Cytosine)
if (clooppos[3] == Adenine)
if (clooppos[4] == Thymine)
if (s[-1] == Guanine)
if (*s == Thymine)
if (s[1] == Thymine)
energy += 1.0;
}
if (RI[b9])
{
if (b8 == Thymine)
{
if (clooppos[1] == Thymine)
{
if (cloopend[-2] == Adenine)
{
if (wcbp[dpos[1]][dpos[darm-2]])
{
if (*clooppos == Cytosine)
{
if (abondtype < 0x200)
energy += 1.0;
if (bondtype < 0x10000)
if (dtbondtype < 0x200)
if (agcat >= 3)
if (cgcat >= 4)
if (tl < 10)
if (var < 6)
if (spacer1 == 2)
if (spacer2 == 1)
if (tstem >= 3)
energy += 3.0;
}
if (tstem >= 5)
if (s[-1] == Guanine)
if (*s == Thymine)
if (s[1] == Thymine)
{ energy += 1.0;
if (tl >= 5)
if (spacer1 == 2)
if (spacer2 == 1)
if (tbondtype < 0x100)
if (wcbp[dpos[dstem+1]][b48])
energy += 3.0; }
if (tstem >= 3)
if (tl < 10)
if (spacer1 == 2)
if (spacer2 == 1)
if (RI[cloopend[-1]])
if (dl > 2)
if (var >= 2)
if (var < 6)
if (ggbp[dpos[dstem+1]][b48])
{
if (dtbondtype < 0x100)
{ energy += 3.5;
if ((bondtype & 0xf00) == 0)
if (*clooppos == Cytosine)
energy += 1.5; }
if (bondtype < 0x10000)
if (tstem > 2)
if (tbondtype < 0x200) energy += 2.5;
if (abondtype < 0x100)
if (wcbp[dpos[2]][dpos[darm-3]])
energy += 3.0;
if (tbondtype < 0x100)
if (agcat >= 6)
if (tstem >= 5)
if ((tbondtype & 0xf) > 0)
if (RI[cloopend[-1]])
if (cgcat >= 4)
energy += 2.0;
}
else
if (!ggstembp[*tpos][apos2[-1]])
if (wcbp[dpos[dstem+1]][*tpos])
energy += 1.5;
}
if ((abondtype & 0xf) < 1)
if (abondtype < 0x100)
if (gcv > 1.2)
if (dl > 3)
if (bp[dpos[dstem+1]][b48])
if (spacer1 == 2)
if (spacer2 == 1)
if (*clooppos == Cytosine)
energy += 5.0;
if (cbondtype < 0x100)
if (tbondtype < 0x100)
if (tstem >= 3)
if (dl > 3)
if (var < 6)
if (bp[dpos[dstem+1]][b48])
if (spacer1 == 2)
if (spacer2 == 1)
energy += 2.5;
}
if (stembp[dpos[dstem+1]][b48])
{
if (*clooppos == Thymine)
if (cloopend[-2] == Guanine)
if (clooppos[2] == Guanine)
if (clooppos[3] == Thymine)
if (clooppos[4] == Guanine)
if (dl > 2)
energy += 1.0;
if (cbondtype < 0x100)
if (dbondtype < 0x10000)
if (wcbp[dpos[1]][dpos[darm-2]])
if (var < 6)
if (tstem >= 3)
if (gcv >= 1.2)
if (dl > 3)
energy += 1.0;
if (tstem >= 5)
if (dtbondtype < 0x200)
if (*clooppos == Cytosine)
if (spacer1 == 2)
if (spacer2 == 1)
if (RI[cloopend[-2]])
energy += 0.5;
}
}
if (tstem > 2)
if (tarm < 28)
if (spacer1 == 2)
if (spacer2 == 1)
if (dl > 3)
if (j < 1)
if (k > ti)
if (ggstembp[dpos[dstem+1]][b48])
energy += 2.5;
if (dtbondtype < 0x100)
if ((tbondtype & 0xf) > 0)
if (bp[dpos[dstem+1]][b48])
if (b9 == Adenine)
if ((dbondtype & 0xf) > 0) energy += 2.0;
else
if (spacer2 == 1)
energy += 0.5;
if (cloopend[-2] == Adenine)
if (cloopend[-1] == Adenine)
if (cbondtype < 0x2000)
if (spacer1 > 1)
if (dl > 2)
if (var < 6)
energy += 0.75;
}
if (var > 2)
if (dl > 2)
{
if (cbondtype < 0x200)
if (((mabondtype & 0xf) > 3) || (bondtype < 0x1000))
{
if (bp[dpos[dstem+1]][b48])
energy += 1.0;
if (cbondtype < 0x100)
if (dbondtype < 0x100)
if (bp[b8][dpos[dstem]])
if (bp[b8][dpos[darm-dstem-1]])
if (var < 6)
if (tstem >= 3)
if (tl < 10)
if (spacer1 == 2)
if (spacer2 == 1)
if (clooppos[1] == Thymine)
if (cloopend[-2] == Adenine)
energy += 3.0;
}
if (clooppos[1] == Thymine)
if (RI[cloopend[-2]])
{
if (*clooppos == Cytosine)
{
if (dtbondtype < 0x200)
if (agcat >= 3)
if (cgcat >= 4)
if (var < 6)
if (tstem >= 3)
if (tl < 10)
if (spacer1 == 2)
if (spacer2 == 1)
{ if (abondtype > 0x20000)
if (bp[dpos[dstem+1]][b48])
energy += 7.0;
if (agcat >= 6) energy += 2.0; }
if ((bondtype & 0xf00) == 0)
if (gcv > 5.0)
if (s[-1] == Guanine)
if (*s == Thymine)
if (tstem >= 5)
if (var < 6)
if (tl < 10)
if (spacer1 == 2)
if (spacer2 == 1)
energy += 2.0;
if (abondtype < 0x100)
if (cbondtype < 0x10000)
if (bp[dpos[dstem+1]][b48])
if (cgcat >= 4)
if (tstem >= 3)
if (var < 6)
if (tstem >= 3)
if (tl < 10)
if (spacer1 == 2)
if (spacer2 == 1)
energy += 1.5;
}
if (dtbondtype < 0x100)
if (agcat >= 4)
if (cgcat >= 4)
if (var < 6)
if (tstem >= 3)
if (tl < 10)
{ if (spacer1 == 2)
{ if (abondtype < 0x3000)
if (stackbp[dpos[dstem+1]][b48])
energy += 3.0;
if (b8 == Thymine)
if (s[-1] == Guanine)
if (*s == Thymine)
if (s[1] == Thymine)
energy += 3.5; }
if (agcat >= 6)
if (YI[*clooppos])
if (s[-1] == Guanine)
if (*s == Thymine)
if ((dtbondtype & 0xf) > 0)
energy += 3.0; }
if (mabondtype < 0x10000)
if (dtbondtype < 0x400)
if (agcat >= 5)
if (cgcat >= 3)
if (tl < 10)
if (var < 6)
if (spacer1 == 2)
if (spacer2 == 1)
{
if (dtbondtype < 0x200)
if (cbondtype < 0x300)
if (bondtype < 0x10000)
if (tstem >= 3)
energy += 1.0;
if (tstem >= 5)
if (s[-1] == Guanine)
energy += 4.0;
}
}
}
}
else
if (bondtype < 0x10000)
if (mabondtype < 0x500)
if (dbondtype < 0x100)
if (b8 == Thymine)
if (agcat >= 4)
if (clooppos[1] == Thymine)
if (cloopend[-2] == Adenine)
if (cloopend[-1] == Adenine)
if (spacer1 == 2)
if (spacer2 == 1)
if (dstem >= 3)
if (tstem >= 5)
if (dl > 2)
if (tl < 10)
if (var < 6)
energy += 7.0;
if (agcat >= 5)
if (cgcat >= 4)
if ((acbondtype & 0xf) >= 3)
{ if (tbondtype < 0x100)
if ((dbondtype & 0xf) > 0)
if ((((dbondtype >> 4) + dbondtype) & 0xf) >= 3)
if (wcbp[dpos[dstem+1]][b48])
if (b8 == Thymine)
if (RI[b9])
if (clooppos[1] == Thymine)
if (YI[*clooppos])
if (RI[cloopend[-2]])
if (RI[cloopend[-1]])
if (spacer1 == 2)
if (spacer2 == 1)
if (dl > 2)
if (tl < 10)
if (var < 6)
if (var > 2)
energy += 6.0;
if (cgcat >= 5)
if (abondtype < 0x10000)
if (bp[dpos[dstem+1]][b48])
if (clooppos[1] == Thymine)
if (YI[*clooppos])
if (RI[cloopend[-2]])
if (dl > 2)
if (tl < 10)
if (var < 6)
if (var > 2)
energy += 6.0; }
if (energy >= dtthresh)
energy -= (0.9*(energy - dtthresh) + 5.0);
else continue; }
/* remember fully formed mttRNA gene if threshold reached */
if (energy < thresh) continue;
te.energy = energy;
thresh = energy;
te.ps = apos1;
te.spacer1 = spacer1;
te.dstem = dstem;
te.dloop = dl;
te.spacer2 = spacer2;
te.cstem = cstem;
te.cloop = cloop;
te.var = var;
te.varbp = (var > 17)?varbp:0;
te.tstem = tstem;
te.tloop = tl;
k = astem + spacer1 + darm + spacer2;
te.anticodon = k + cstem + 2;
te.nintron = 0;
te.intron = 0;
te.nbase = k + carm + var + 2*tstem + tl;
tastem = astem;
tastem8 = astem8;
tastem8d = astem8d;
} }
/* for highest energy mttRNA gene */
/* decide astem length, look for NCCA acceptor tail */
/* and calculate total length */
if (te.ps)
{ apos2 = te.ps + te.nbase;
if (extastem)
if (tastem8d)
{ te.astem1 = 8;
te.astem2 = 8;
te.ps--;
te.nbase++;
te.anticodon++;
as = aatail(apos2+8,&aext,sw); }
else
{ te.astem1 = tastem;
te.astem2 = tastem;
as = aatail(apos2+tastem,&aext,sw);
if (tastem8)
{ as8 = aatail(apos2+8,&aext8,sw);
if (as8 >= as)
{ te.ps--;
te.nbase++;
te.anticodon++;
te.astem1 = 8;
te.astem2 = 8;
as = as8;
aext = aext8; }}}
else
{ te.astem1 = tastem;
te.astem2 = tastem;
as = aatail(apos2+tastem,&aext,sw); }
if (as < 2) aext = 1;
te.nbase += te.astem2;
nbasefext = te.nbase + ASTEM2_EXT;
te.nbase += aext;
/* store mttRNA gene if there are no */
/* higher energy overlapping mttRNA genes */
te.start = (long)(te.ps - seq);
if (tn = find_slot(d,&te,&nts,sw))
{ base_copy3(te.ps,te.seq,nbasefext);
base_copy3(te.ps,te.eseq,nbasefext);
te.aatail = aext;
*tn = te; }}
}
return(nts); }
int tmopt(data_set *d,
trna_loop *th, int tarm, double the,
trna_loop *ahit, int nah,
int nts,int *seq, csw *sw)
{ int r,na,nr,nrh,ibase,flag,as,aext,nbasefext;
int *s,*v,*s1,*s2,*sa,*sb,*se,*sf,*ps,*tpos,pseq[MAXETRNALEN+1];
static int gtemplate[6] = { 0x00,0x00,0x11,0x00,0x00,0x00 };
static double A[6] = { 6.0,0.0,0.0,0.0,0.0,0.0 };
static double Ar[6] = { 10.0,0.0,0.0,0.0,0.0,0.0 };
static double Cr[6] = { 0.0,10.0,0.0,0.0,0.0,0.0 };
static double G[6] = { 0.0,0.0,6.0,0.0,0.0,0.0 };
static double Ga[6] = { 0.0,0.0,7.0,0.0,0.0,0.0 };
static double K[6] = { 0.0,0.0,6.0,6.0,0.0,0.0 };
static double Tr[6] = { 0.0,0.0,0.0,10.0,0.0,0.0 };
double e,energy,penergy,tenergy,aenergy,athresh,cthresh,cathresh;
static double bem[6][6] =
{ { -1.072,-0.214,-1.072, ATBOND, 0.000, 0.000 },
{ -0.214,-1.072, 3.000,-1.072, 0.000, 0.000 },
{ -1.072, 3.000,-1.072, 1.286, 0.000, 0.000 },
{ ATBOND,-1.072, 1.286,-0.214, 0.000, 0.000 },
{ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000 },
{ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000 } };
static trna_loop rhit[NH];
gene te,*tn;
static gene t =
{ "",{TERM},{TERM},NULL,0,0,0L,0L,7,7,1,0,0,0,13,8,0,28,0,0,3,0,5,7,
tmRNA,0.0,0,0,0 };
tpos = th->pos;
flag = 0;
te.energy = sw->tmrnathresh;
athresh = sw->tmathresh;
cthresh = sw->tmcthresh;
cathresh = sw->tmcathresh;
s = tpos + tarm + 4;
v = tpos + th->stem - 10;
energy = K[*v] + G[v[1]] + A[v[2]];
e = K[v[1]] + G[v[2]] + A[v[3]];
if (e > energy) energy = e;
if (energy < 18.0) energy = 0.0;
tenergy = Tr[*s]+Cr[s[1]]+Cr[s[2]]+Ar[s[3]] + energy + 1.59*the;
nrh = find_resume_seq(tpos-MAXTPTSDIST,TPWINDOW,rhit,NH,sw);
nr = -1;
while (++nr < nrh)
{ ps = rhit[nr].pos;
penergy = tenergy + rhit[nr].energy - 0.001*((double)(tpos - ps));
if (rhit[nr].stem < 24) penergy -= 15.0;
na = -1;
while (++na < nah)
{ aenergy = ahit[na].energy;
if (aenergy < athresh) continue;
t.ps = ahit[na].pos;
if (t.ps < (ps - MAXTPDIST)) continue;
if (t.ps > (ps - MINTPDIST)) break;
energy = -INACTIVE;
sa = t.ps + t.astem1;
for (sb=sa+9, se=sb+t.cstem; sb <= (sa+16); sb++,se++)
for (sf = tpos-3; sf >= (tpos-7); sf--)
{ s1 = sb;
s2 = sf;
e = bem[*s1++][*--s2];
while (s1 < se) e += bem[*s1++][*--s2];
if (e > energy)
{ energy = e;
t.var = (int)(tpos - sf);
t.dloop = (int)(sb - sa); }}
if (energy < cthresh) continue;
energy += aenergy;
if (energy < cathresh) continue;
sb = sa + 3;
sf = sa + 7;
r = gtemplate[*sb++];
while (sb < sf)
{ r = (r >> 4) + gtemplate[*sb++];
if ((r & 3) == 2)
{ energy += 14.0;
break; }}
t.energy = penergy + Ga[t.ps[1]] + Ga[t.ps[2]] + energy;
if (t.energy > te.energy)
{ flag = 1;
t.tstem = th->stem;
t.tloop = th->loop;
t.tps = (int)(ps - t.ps);
t.tpe = t.tps + rhit[nr].stem;
ibase = (int)(tpos - t.ps);
t.nintron = ibase - t.var - 2*t.cstem -
t.dloop - t.astem1;
t.nbase = ibase + tarm + t.astem2 - t.nintron;
te = t; }}}
if (flag)
{ te.start = (long)(te.ps - seq);
s = te.ps + te.nbase + te.nintron;
as = aatail(s,&aext,sw);
nbasefext = te.nbase + ASTEM2_EXT;
te.nbase += aext;
tn = find_slot(d,&te,&nts,sw);
if (tn)
{ te.intron = te.astem1 + te.dloop + te.cstem;
te.asst = 0;
base_copy3(te.ps,te.eseq,nbasefext+te.nintron);
remove_intron(te.ps,pseq,nbasefext,
te.intron,te.nintron);
base_copy3(pseq,te.seq,te.nbase);
te.aatail = aext;
*tn = te; }}
return(nts); }
int tmopt_perm(data_set *d,
trna_loop *th, int tarm, double the,
trna_loop *ahit, int nah,
int nts, int *seq, csw *sw)
{ int r,na,nr,nrh,flag,as,aext;
int *s,*v,*s1,*s2,*sa,*sb,*se,*sf,*ps,*apos,*tpos;
static int gtemplate[6] = { 0x00,0x00,0x11,0x00,0x00,0x00 };
double e,energy,penergy,tenergy,aenergy,athresh,cthresh,cathresh;
static double A[6] = { 6.0,0.0,0.0,0.0,0.0,0.0 };
static double Ar[6] = { 10.0,0.0,0.0,0.0,0.0,0.0 };
static double Cr[6] = { 0.0,10.0,0.0,0.0,0.0,0.0 };
static double G[6] = { 0.0,0.0,6.0,0.0,0.0,0.0 };
static double Ga[6] = { 0.0,0.0,7.0,0.0,0.0,0.0 };
static double K[6] = { 0.0,0.0,6.0,6.0,0.0,0.0 };
static double Tr[6] = { 0.0,0.0,0.0,10.0,0.0,0.0 };
static double bem[6][6] =
{ { -1.072,-0.214,-1.072, ATBOND, 0.000, 0.000 },
{ -0.214,-1.072, 3.000,-1.072, 0.000, 0.000 },
{ -1.072, 3.000,-1.072, 1.286, 0.000, 0.000 },
{ ATBOND,-1.072, 1.286,-0.214, 0.000, 0.000 },
{ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000 },
{ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000 } };
static trna_loop rhit[NH];
gene te,*tn;
static gene t =
{ "",{TERM},{TERM},NULL,0,0,0L,0L,7,7,1,0,0,0,13,8,0,28,0,0,3,0,5,7,
tmRNA,0.0,0,0,0 };
tpos = th->pos;
flag = 0;
te.energy = sw->tmrnathresh;
athresh = sw->tmathresh;
cthresh = sw->tmcthresh;
cathresh = sw->tmcathresh;
s = tpos + tarm + 4;
v = tpos + th->stem - 10;
energy = K[*v] + G[v[1]] + A[v[2]];
e = K[v[1]] + G[v[2]] + A[v[3]];
if (e > energy) energy = e;
if (energy < 18.0) energy = 0.0;
tenergy = Tr[*s]+Cr[s[1]]+Cr[s[2]]+Ar[s[3]]+ energy + 1.59*the;
na = -1;
while (++na < nah)
{ aenergy = ahit[na].energy;
if (aenergy < athresh) continue;
apos = ahit[na].pos;
if (apos < (tpos + MINTSTEM_DIST)) continue;
if (apos > (tpos + MAXTSTEM_DIST + MAXPPINTRONDIST)) break;
energy = -INACTIVE;
sa = apos + t.astem1;
for (sb=sa+9, se=sb+t.cstem; sb <= (sa+16); sb++,se++)
for (sf = tpos-3; sf >= (tpos-7); sf--)
{ s1 = sb;
s2 = sf;
e = bem[*s1++][*--s2];
while (s1 < se) e += bem[*s1++][*--s2];
if (e > energy)
{ energy = e;
t.var = (int)(tpos - sf);
t.dloop = (int)(sb - sa); }}
if (energy < cthresh) continue;
energy += aenergy;
if (energy < cathresh) continue;
sb = sa + 3;
sf = sa + 7;
r = gtemplate[*sb++];
while (sb < sf)
{ r = (r >> 4) + gtemplate[*sb++];
if ((r & 3) == 2)
{ energy += 14.0;
break; }}
penergy = tenergy + Ga[apos[1]] + Ga[apos[2]] + energy;
nrh = find_resume_seq(apos+MINTPDIST,TPWINDOW,rhit,NH,sw);
nr = -1;
while (++nr < nrh)
{ ps = rhit[nr].pos;
t.energy = penergy + rhit[nr].energy;
if (rhit[nr].stem < 24) t.energy -= 15.0;
if (t.energy > te.energy)
{ flag = 1;
t.tstem = th->stem;
t.tloop = th->loop;
t.asst = (long)(apos - tpos) + t.var + t.cstem;
t.ps = tpos - t.var - t.cstem;
t.tps = (int)(ps - t.ps);
t.tpe = t.tps + rhit[nr].stem;
te = t; }}}
if (flag)
{ te.start = (long)(te.ps - seq) - 54;
te.intron = te.cstem + te.var + 2*te.tstem + te.tloop +
te.astem2;
as = aatail(te.ps + te.intron,&aext,sw);
te.aatail = aext;
base_copy3(te.ps-54,te.eseq,te.tpe+1+TMPTRAILER);
te.nbase = te.astem1 + te.dloop + te.cstem;
base_copy3(te.ps+te.asst,te.seq,te.nbase);
base_copy3(te.ps,te.seq+te.nbase,te.intron + ASTEM2_EXT);
te.intron += aext;
te.nbase += te.intron;
te.nintron = te.tpe - te.nbase + 1 + TMPTRAILER;
te.intron += 54;
te.tps += 54;
te.tpe += 54;
te.asst += 54;
tn = find_slot(d,&te,&nts,sw);
if (tn) *tn = te; }
return(nts); }
int ti_genedetected(data_set *d, int nts, int *seq, gene *te, csw *sw)
{ int as,aext,as8,aext8,nbasefext,*s;
int pseq[2*MAXETRNALEN+1];
gene *tn;
te->nbase = te->astem1 + te->spacer1 + te->spacer2 + 2*te->dstem +
te->dloop + 2*te->cstem + te->cloop +
te->var + 2*te->tstem + te->tloop + te->astem2;
s = te->ps + te->nbase + te->nintron;
as = aatail(s,&aext,sw);
if (sw->extastem)
if (te->astem1 == 7)
if (bp[te->ps[-1]][*s])
{ as8 = aatail(s+1,&aext8,sw);
if (as8 >= as)
{ te->ps--;
te->nbase += 2;
te->anticodon++;
if (te->nintron > 0) te->intron++;
te->astem1 = 8;
te->astem2 = 8;
as = as8;
aext = aext8; }}
nbasefext = te->nbase + ASTEM2_EXT;
te->nbase += aext;
te->start = (long)(te->ps - seq);
tn = find_slot(d,te,&nts,sw);
if (tn)
{ if (te->nintron == 0)
base_copy3(te->ps,te->seq,nbasefext);
else
{ base_copy3(te->ps,te->eseq,nbasefext + te->nintron);
remove_intron(te->ps,pseq,nbasefext,
te->intron,te->nintron);
base_copy3(pseq,te->seq,nbasefext); }
te->aatail = aext;
*tn = *te; }
return(nts); }
int tmioptimise(data_set *d, int *seq, int lseq, int nts, csw *sw)
{ int i,j,k,intron,nt,nth,nd1,nd2,ndx,ndh,na,nah,nppah,nc,nch,tfold,tarm;
int dstem,dloop,flag,mindist,maxdist,tmindist,tmaxdist,tmmindist,tmmaxdist;
int tarmthresh,tmstrict,sp2min,sp2max,ige[7];
int *se,*sc,*sb,*si,*tpos,*tend,*apos,*dpos,*tloopfold,*tmv,*cend;
int *s1,*s2,*sd,*sf,*sl,*sg1,*sg2,*cposmin,*cposmax,*cpos;
unsigned int r,q,c;
double e,ec,he,the,thet,ethresh,energy,cenergy,denergy,ienergy;
double tdarmthresh,genergy,energy2,energyf,energyf6;
static unsigned int TT[6] =
{ 0x00, 0x00, 0x00, 0x11, 0x00, 0x00 };
static unsigned int GG[6] =
{ 0x00, 0x00, 0x11, 0x00, 0x00, 0x00 };
static unsigned int ct[6] = { 0,0,0,0,0,0 };
static unsigned int cA[6] = { 0,0,0,2,0,0 };
static unsigned int cC[6] = { 0,0,2,0,0,0 };
static unsigned int cG[6] = { 0,2,0,1,0,0 };
static unsigned int cT[6] = { 2,0,1,0,0,0 };
static int yic[9] = { 1,0,0,0,0,0,0,0,0 };
static int tic[9] = { 1,1,0,0,0,0,0,0,0 };
static int a1ic[9] = { 1,1,1,0,0,0,0,0,0 };
static int a2ic[9] = { 1,1,1,1,0,0,0,0,0 };
static int a3ic[9] = { 1,1,1,1,1,0,0,0,0 };
static int ric[9] = { 1,1,1,1,1,1,0,0,0 };
static int goffb[13] = { 0,0,0,0,1,2,2,2,2,2,2,2,2 };
static int goffe[13] = { 0,0,0,0,2,3,4,4,5,6,6,6,6 };
static int cY[6] = { 0,1,0,1,0,0 };
static int cR[6] = { 1,0,1,0,0,0 };
static double ilw = 0.002;
static double G[6] = { 0.0,0.0,6.0,0.0,0.0,0.0 };
static double T[6] = { 0.0,0.0,0.0,7.0,0.0,0.0 };
static double Y[6] = { 0.0,3.0,0.0,3.0,0.0,0.0 };
static double R[6] = { 2.0,0.0,2.0,0.0,0.0,0.0 };
static double YP[6] = { 0.0,3.0,0.0,3.0,0.0,0.0 };
static double RP[6] = { 2.0,0.0,2.0,0.0,0.0,0.0 };
static double RI[6] = { 0.1,0.0,0.05,0.0,0.0,0.0 };
static double GI[6] = { 0.0,0.0,0.1,0.0,0.0,0.0 };
static double YI[6] = { 0.0,0.1,0.0,0.1,0.0,0.0 };
static double AI[6] = { 1.0,0.0,0.0,0.0,0.0,0.0 };
static double GC[6] = { 0.0,1.5,6.0,0.0,0.0,0.0 };
static double G3[6] = { 0.0,6.0,12.0,12.0,0.0,0.0 };
static double dR[6] = { 6.0,0.0,6.0,0.0,0.0,0.0 };
static double RH[6] = { 3.0,0.0,3.0,0.0,0.0,0.0 };
static double AGT[6] = { 6.0,0.0,6.0,6.0,0.0,0.0 };
static double dT[6] = { 0.0,0.0,0.0,6.0,0.0,0.0 };
static double dbem[6][6] =
{ { -2.144,-0.428,-2.144, ATBOND, 0.000, 0.000 },
{ -0.428,-2.144, 3.000,-2.144, 0.000, 0.000 },
{ -2.144, 3.000,-2.144, 1.286, 0.000, 0.000 },
{ ATBOND,-2.144, 1.286,-0.428, 0.000, 0.000 },
{ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000 },
{ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000 } };
static double dfem[6][6] =
{ { -4.000,-4.000,-4.000, ATBOND, 0.000, 0.000 },
{ -4.000,-4.000, 3.000,-4.000, 0.000, 0.000 },
{ -4.000, 3.000,-4.000, 1.286, 0.000, 0.000 },
{ ATBOND,-4.000, 1.286,-4.000, 0.000, 0.000 },
{ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000 },
{ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000 } };
static double cbem[6][6] =
{ { -1.072,-0.214,-1.072,2.0*ATBOND, 0.000, 0.000 },
{ -0.214,-1.072, 6.000,-1.072, 0.000, 0.000 },
{ -1.072, 6.000,-1.072, 3.400, 0.000, 0.000 },
{ 2.0*ATBOND,-1.072, 3.400,-0.214, 0.000, 0.000 },
{ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000 },
{ 0.000, 0.000, 0.000, 0.000, 0.000, 0.000 } };
static trna_loop thit[NTH],chit[NC],ahit[NA];
static trna_dloop dhit[ND];
gene te;
static gene t =
{ "",{TERM},{TERM},NULL,0,0,0L,0L,7,7,1,2,1,3,9,5,7,0,0,0,15,0,5,7,
tRNA,0.0,0,0,0 };
if (sw->mtrna)
{ nts = find_mt_trna(d,seq,lseq,nts,sw);
if (!sw->tmrna) return(nts); }
ethresh = sw->trnathresh;
tmmindist = MINTPTSDIST + MINTPDIST;
tmmaxdist = MAXTPTSDIST + MAXTPDIST;
tmindist = (MINTRNALEN + sw->minintronlen - MAXTSTEM_DIST);
tmaxdist = (MAXTRNALEN + sw->maxintronlen - MINTSTEM_DIST);
if (sw->trna)
{ if (sw->tmrna)
{ mindist = (tmindist < tmmindist)?tmindist:tmmindist;
maxdist = (tmaxdist > tmmaxdist)?tmaxdist:tmmaxdist; }
else
{ mindist = tmindist;
maxdist = tmaxdist; }}
else
{ mindist = tmmindist;
maxdist = tmmaxdist; }
tarmthresh = sw->ttarmthresh;
tdarmthresh = sw->tdarmthresh;
tmstrict = sw->tmstrict;
sp2min = sw->sp2min;
sp2max = sw->sp2max;
nth = find_tstems(seq,lseq,thit,NTH,sw);
nt = -1;
while (++nt < nth)
{ tpos = thit[nt].pos;
t.tloop = thit[nt].loop;
t.tstem = thit[nt].stem;
tfold = tpos[-1];
tloopfold = tpos + t.tstem + 1;
tarm = 2*t.tstem + t.tloop;
tend = tpos + tarm;
tmv = tpos - VARMIN;
flag = 0;
te.energy = ethresh;
the = thit[nt].energy;
nah = find_astem5(tpos-maxdist,tpos-mindist,tend,7,ahit,NA,sw);
if (sw->tmrna)
{ thet = the - G[tpos[t.tstem]] - G[tpos[t.tstem+1]];
if (tmstrict)
{ if (thet >= tarmthresh)
nts = tmopt(d,thit+nt,tarm,thet,ahit,nah,nts,seq,sw); }
else
nts = tmopt(d,thit+nt,tarm,the,ahit,nah,nts,seq,sw);
nppah = find_astem5(tpos+MINPPASDIST,tpos+MAXPPASDIST,
tend,7,ahit+nah,NA-nah,sw);
nts = tmopt_perm(d,thit+nt,tarm,the,ahit+nah,nppah,nts,seq,sw);
if (thet < tarmthresh) continue;
the = thet; }
if (!sw->trna) continue;
na = -1;
while (++na < nah)
{ apos = ahit[na].pos;
if (apos < (tpos - tmaxdist)) continue;
if (apos > (tpos - tmindist)) break;
he = the + ahit[na].energy;
/* find dstems */
ndh = 0;
sc = apos + 8;
energyf = dfem[sc[5]][tfold];
sl = sc + sw->sp1max;
while (sc < sl)
{ energy2 = dT[sc[-2]] + RH[*(sc-1)] + GC[*sc] + dfem[sc[-2]][sc[4]];
energyf6 = dfem[sc[6]][tfold];
for (dstem = 3; dstem <= 4; dstem++)
{ sd = sc + dstem;
dloop = 3;
se = sd + dloop;
energy = energy2 + 6.0 + dR[*(se-1)] + energyf;
if (dstem == 3)
if (energyf < 0.0) energyf = energyf6;
se += dstem;
s1 = sc;
s2 = se;
sf = s1 + dstem;
while (s1 < sf) energy += dbem[*s1++][*--s2];
if (energy >= tdarmthresh)
{ if (ndh >= ND) goto DFL;
dhit[ndh].pos = sc;
dhit[ndh].end = se;
dhit[ndh].loop = dloop;
dhit[ndh].stem = dstem;
dhit[ndh].energy = energy;
ndh++; }
sg1 = sd + 1;
sg2 = sd + 6;
q = GG[*sg1++];
ige[1] = q & 3;
j = 2;
while (sg1 <= sg2)
{ q = (q >> 4) + GG[*sg1++];
ige[j++] = q & 3; }
for (dloop = 4; dloop <= 11; dloop++)
{ j = goffb[dloop];
k = goffe[dloop];
c = ige[j++];
while (j <= k) c = c | ige[j++];
genergy = G3[c];
se = sd + dloop;
energy = energy2 + genergy + dR[*(se-1)] + energyf;
se += dstem;
s1 = sc;
s2 = se;
sf = s1 + dstem;
while (s1 < sf) energy += dbem[*s1++][*--s2];
if (energy >= tdarmthresh)
{ if (ndh >= ND) goto DFL;
dhit[ndh].pos = sc;
dhit[ndh].end = se;
dhit[ndh].loop = dloop;
dhit[ndh].stem = dstem;
dhit[ndh].energy = energy;
ndh++; }}}
s1 = sc;
s2 = sc + 16;
sd = sc + 6;
j = bp[*s1][*--s2];
while (++s1 < sd) j += bp[*s1][*--s2];
if (j >= 6)
{ energy = dT[sc[-1]] + RH[*sc] + GC[*(sc+1)] + energyf6;
energy += G[*++sd];
energy += G[*++sd];
energy += AGT[*++sd] + dfem[sc[-1]][sc[4]];
sd += 7;
s1 = sc;
s2 = sd;
sf = s1 + 6;
while (s1 < sf) energy += dbem[*s1++][*--s2];
if (energy >= tdarmthresh)
{ if (ndh >= ND) goto DFL;
dhit[ndh].pos = sc;
dhit[ndh].end = sd;
dhit[ndh].loop = 4;
dhit[ndh].stem = 6;
dhit[ndh].energy = energy;
ndh++; }}
s1 = sc;
s2 = sc + 18;
sd = sc + 7;
j = bp[*s1][*--s2];
while (++s1 < sd) j += bp[*s1][*--s2];
if (j >= 7)
{ energy = energy2 + dfem[sc[7]][tfold];
energy += G[*++sd];
energy += G[*++sd];
energy += AGT[*++sd];
sd += 8;
s1 = sc;
s2 = sd;
sf = s1 + 7;
while (s1 < sf) energy += dbem[*s1++][*--s2];
if (energy >= tdarmthresh)
{ if (ndh >= ND) goto DFL;
dhit[ndh].pos = sc;
dhit[ndh].end = sd;
dhit[ndh].loop = 4;
dhit[ndh].stem = 7;
dhit[ndh].energy = energy;
ndh++; }}
energyf = energyf6;
sc++; }
goto DFN;
DFL:
fprintf(stderr,"Too many D-stem hits\n");
DFN:
/* End of find dstems routine */
nd1 = ndh;
while (--nd1 >= 0)
{ dstem = dhit[nd1].stem;
dpos = dhit[nd1].pos;
if ((int)(dpos - apos) < 9)
dhit[nd1].energy -= 3.0;
if (*tloopfold == Guanine)
{ sb = dpos + dstem + 2;
sc = sb;
se = sb + t.dloop - 3;
r = TT[*sb++];
while (sb < se)
{ r = (r >> 4) + TT[*sb++];
if (r & 2)
{ dhit[nd1].energy += 10.0;
break; }}
r = GG[*sc++];
while (sc < se)
{ r = (r >> 4) + GG[*sc++];
if (r & 2)
{ dhit[nd1].energy -= 12.0;
break; }}}}
nd1 = ndh;
while (--nd1 >= 0)
{ if (!dhit[nd1].end) continue;
cpos = dhit[nd1].end;
denergy = dhit[nd1].energy;
ndx = nd1;
nd2 = nd1;
while (--nd2 >= 0)
{ if (dhit[nd2].end != cpos) continue;
e = dhit[nd2].energy;
if (e > denergy)
{ denergy = e;
dhit[ndx].end = NULL;
ndx = nd2; }}}
nd1 = ndh;
while (--nd1 >= 0)
{ if (!dhit[nd1].end) continue;
cposmin = dhit[nd1].end;
cposmax = cposmin;
break; }
nd2 = nd1;
while (--nd2 >= 0)
{ if (!(cpos = dhit[nd2].end)) continue;
if (cpos < cposmin) cposmin = cpos;
if (cpos > cposmax) cposmax = cpos; }
for (cpos = cposmin + sp2min; cpos <= (cposmax + sp2max); cpos++)
{ denergy = -INACTIVE;
ndx = -1;
nd1 = ndh;
while (--nd1 >= 0)
{ if (!dhit[nd1].end) continue;
if ((dhit[nd1].end + sp2max) < cpos) continue;
if ((dhit[nd1].end + sp2min) > cpos) continue;
e = dhit[nd1].energy;
if (e > denergy)
{ denergy = e;
ndx = nd1; }}
if (ndx < 0) continue;
denergy += he;
if (denergy < (te.energy - 49.0)) continue;
/* find cstems */
nch = 0;
si = cpos;
sc = cpos + 5;
se = cpos + 4;
ct[0] = cA[*se];
ct[1] = cC[*se];
ct[2] = cG[*se];
ct[3] = cT[*se];
while (--se >= cpos)
{ ct[0] = (ct[0] << 4) + cA[*se];
ct[1] = (ct[1] << 4) + cC[*se];
ct[2] = (ct[2] << 4) + cG[*se];
ct[3] = (ct[3] << 4) + cT[*se]; }
si += 11;
se = tmv - VARDIFF - 5;
if (si < se) si = se;
r = ct[*si++];
r = (r >> 4) + ct[*si++];
r = (r >> 4) + ct[*si++];
r = (r >> 4) + ct[*si++];
while (si < tmv)
{ r = (r >> 4) + ct[*si++];
if ((r & 0xf) >= 5)
{ if (nch >= NC)
{ fprintf(stderr,"Too many cstem hits\n");
goto FN; }
chit[nch].pos = si;
chit[nch].stem = 5;
chit[nch].loop = (int)(si - sc - 5);
if (chit[nch].loop == 9)
if (bp[*sc][si[-6]])
if (cY[sc[2]])
if (cR[sc[6]])
if (cY[sc[1]])
{ chit[nch].stem = 6;
chit[nch].loop = 7; }
s1 = cpos;
s2 = si;
se = s1 + chit[nch].stem;
chit[nch].energy = cbem[*s1++][*--s2];
while (s1 < se)
chit[nch].energy += cbem[*s1++][*--s2];
nch++; }}
FN:
/* end of find cstems routine */
nc = -1;
while (++nc < nch)
{ energy = denergy + chit[nc].energy;
if (energy < (te.energy - 19.0)) continue;
cend = chit[nc].pos;
t.var = (int)(tpos - cend);
t.cloop = chit[nc].loop;
t.cstem = chit[nc].stem;
intron = 0;
if (t.cloop < 9)
{ if (sw->minintronlen > 0) continue;
if (sw->cloop7)
if (t.cloop != 7) continue;
t.nintron = 0;
if (t.var > 17) energy += vloop_stability(cend,t.var,&t.varbp);
sb = cpos + t.cstem;
energy += T[*(sb + 1)] + Y[*(sb)] + R[*(sb + 5)] -
0.05*t.var - ((t.cloop == 7)?0.0:6.0); }
else
{ t.nintron = t.cloop - 7;
if (t.nintron > sw->maxintronlen) continue;
if (t.nintron < sw->minintronlen) continue;
if (t.var > 17) energy += vloop_stability(cend,t.var,&t.varbp);
if (energy < (te.energy - 9.0)) continue;
t.cloop = 7;
sb = cpos + t.cstem;
se = sb + t.nintron;
if (sw->ifixedpos)
{ intron = 6;
cenergy = YP[*sb] + T[sb[1]] + RP[sb[5]]; }
else
{ cenergy = YP[*se] + T[*(se+1)] + RP[*(se+5)];
ienergy = cenergy + RI[*sb] + GI[*(se-1)] +
AI[se[-2]]*YI[se[-1]];
for (j = 1; j <= 7; j++)
{ si = se + j - 1;
ec = YP[*(sb + yic[j]*t.nintron)] +
T[*(sb + tic[j]*t.nintron + 1)] +
RP[*(sb + ric[j]*t.nintron + 5)];
e = ec + RI[*(sb + j)] + GI[*si] + AI[si[-1]]*YI[*si];
if (j == 6) e += 0.01;
if (e > ienergy)
{ ienergy = e;
cenergy = ec;
intron = j; }}}
energy += cenergy - 10.0 - ilw*(t.nintron + 1.1*t.var);
if (t.nintron >= 130)
{ si = se + intron;
j = si[-1];
if (j != Guanine)
{ if (si[-2] != Adenine) energy -= 4.0;
if (j != Cytosine)
if (j != Thymine)
energy -= 8.0; }}}
dstem = dhit[ndx].stem;
dpos = dhit[ndx].pos;
if (dstem >= 6)
{ if (sb[2 + a1ic[intron]*t.nintron] != Thymine) continue;
if (sb[3 + a2ic[intron]*t.nintron] != Cytosine) continue;
if (sb[4 + a3ic[intron]*t.nintron] != Adenine) continue;
energy += 3.0; }
else
if (!(dpos[-1] & 5))
{ i = 0;
si = cend;
se = cend + 4;
while (si < se)
{ if (!(*si++ & 5))
{ if (++i >= 2)
{ energy += 3.0;
break; }}
else
i = 0; }}
if (t.cstem >= 6)
{ if (sb[2 + a1ic[intron]*t.nintron] == Cytosine)
if (sb[3 + a2ic[intron]*t.nintron] == Thymine)
if (sb[4 + a3ic[intron]*t.nintron] == Adenine)
energy += 4.0; }
if (energy < ethresh) continue;
t.energy = energy;
t.astem1 = (t.dstem < 6)?7:((t.tstem < 5)?9:8);
t.astem2 = t.astem1;
t.ps = apos + 7 - t.astem1;
t.nbase = (int)(tend - t.ps) + t.astem2;
t.dstem = dstem;
t.dloop = dhit[ndx].loop;
t.spacer1 = (int)(dpos - apos) - 7;
t.spacer2 = (int)(cpos - dhit[ndx].end);
j = (int)(cpos - t.ps) + t.cstem;
t.anticodon = j + 2;
if (t.nintron > 0)
{ t.intron = j + intron;
if ((t.nbase + t.nintron) > MAXTRNALEN)
{ nts = ti_genedetected(d,nts,seq,&t,sw);
continue; }}
if (energy < te.energy) continue;
flag = 1;
te = t; } }}
if (flag) nts = ti_genedetected(d,nts,seq,&te,sw); }
return(nts); }
void disp_ftable_entry(FILE *f, int n[], int i, int m, csw *sw)
{ if (m > 0)
switch(sw->geneticcode)
{ case METAZOAN_MT:
if (i < 2) fprintf(f," %-4s %-4d",aa(n,sw),m);
else fprintf(f," %-18s %-4d",aa(n,sw),m);
break;
case STANDARD:
case VERTEBRATE_MT:
default:
fprintf(f," %-4s %-5d",aa(n,sw),m);
break; }
else
switch(sw->geneticcode)
{ case METAZOAN_MT:
if (i < 2) fprintf(f," %-4s ",aa(n,sw));
else fprintf(f," %-18s ",aa(n,sw));
break;
case STANDARD:
case VERTEBRATE_MT:
default:
fprintf(f," %-4s ",aa(n,sw));
break; }}
void disp_freq_table(int nt, csw *sw)
{ int i,j,k,m,ambig,*s,c1,c2,c3,c[3],n[3],table[4][4][4];
static int cgflip[4] = { 0,2,1,3 };
FILE *f = sw->f;
ambig = 0;
for (i = 0; i < 4; i++)
for (j = 0; j < 4; j++)
for (k = 0; k < 4; k++)
table[i][j][k] = 0;
for (i = 0; i < nt; i++)
if (ts[i].energy >= 0.0)
if (ts[i].genetype == tRNA)
if (ts[i].cloop == 7)
{ s = ts[i].seq + ts[i].anticodon;
c1 = *s;
c2 = s[1];
c3 = s[2];
if ((c1 >= Adenine) && (c1 <= Thymine))
if ((c2 >= Adenine) && (c2 <= Thymine))
if ((c3 >= Adenine) && (c3 <= Thymine))
table[*s][s[1]][s[2]]++;
else ambig++;
else ambig++;
else ambig++; }
else ambig++;
fprintf(f,"tRNA Anticodon Frequency\n");
for (j = 0; j < 4; j++)
{ n[2] = cgflip[j];
for (k = 0; k < 4; k++)
{ n[1] = cgflip[k];
for (i = 0; i < 4; i++)
{ n[0] = cgflip[i];
fprintf(f,"%c%c%c",cpbase(n[0]),cpbase(n[1]),cpbase(n[2]));
m = table[n[0]][n[1]][n[2]];
disp_ftable_entry(f,n,i,m,sw); }
fputc('\n',f); }}
if (ambig > 0) fprintf(f,"Ambiguous: %d\n",ambig);
fprintf(f,"\ntRNA Codon Frequency\n");
for (i = 0; i < 4; i++)
{ n[0] = 3 - cgflip[i];
for (j = 0; j < 4; j++)
{ n[1] = 3 - cgflip[j];
for (k = 0; k < 4; k++)
{ n[2] = 3 - cgflip[k];
fprintf(f,"%c%c%c",cpbase(n[0]),cpbase(n[1]),cpbase(n[2]));
c[0] = 3 - n[2];
c[1] = 3 - n[1];
c[2] = 3 - n[0];
m = table[c[0]][c[1]][c[2]];
disp_ftable_entry(f,c,k,m,sw); }
fputc('\n',f); }}
if (ambig > 0) fprintf(f,"Ambiguous: %d\n",ambig);
fputc('\n',f); }
void disp_energy_stats(data_set *d, int nt, csw *sw)
{ int i,n[NS],genetype,introns,nintron,trna,mtrna,ntv,nd,nps;
double gc,gcmin[NS],gcmax[NS];
static char genetype_name[NS][30] =
{ "tRNA genes","tmRNA genes","srpRNA genes","rRNA genes","CDS genes","Overall" };
FILE *f = sw->f;
mtrna = sw->mtrna;
trna = sw->trna | mtrna;
nps = 0;
if (mtrna)
{ ntv = 0;
nd = 0; }
if ((sw->trna) && (sw->maxintronlen > 0))
{ introns = 1;
nintron = 0; }
else
introns = 0;
for (i = 0; i < NS; i++)
{ n[i] = 0;
gcmin[i] = 1.0;
gcmax[i] = 0.0; }
for (i = 0; i < nt; i++)
if (ts[i].energy >= 0.0)
{ n[NS-1]++;
genetype = ts[i].genetype;
n[genetype]++;
if (pseudogene(ts + i)) nps++;
if (genetype == tRNA)
{ if (mtrna)
{ if (ts[i].tstem == 0) ntv++;
if (ts[i].dstem == 0) nd++; }
if (introns) if (ts[i].nintron > 0) nintron++;
gc = gc_content(ts+i);
if (gc < gcmin[genetype]) gcmin[genetype] = gc;
if (gc > gcmax[genetype]) gcmax[genetype] = gc; }}
fputc('\n',f);
fputc('\n',f);
if (sw->repeatsn)
if ((n[tRNA] + n[tmRNA]) > 0)
fprintf(f,"%s\n\n",d->seqname);
if (trna)
{ sw->ngene[tRNA] += n[tRNA];
if (n[tRNA] > 3) disp_freq_table(nt,sw);
if ((n[tRNA] > 1) || ((sw->tmrna) && (n[tmRNA] > 0)))
{ if (introns)
{ if (sw->minintronlen == 0)
fprintf(f,"Number of tRNA genes with no introns = %d\n",
n[0]-nintron);
fprintf(f,"Number of tRNA genes with C-loop introns = %d\n",
nintron); }
else
fprintf(f,"Number of %s = %d\n",genetype_name[tRNA],n[tRNA]);
if (mtrna)
{ if (sw->tvloop)
fprintf(f,"Number of TV replacement loop tRNA genes = %d\n",
ntv);
fprintf(f,"Number of D replacement loop tRNA genes = %d\n",
nd); }
if (n[tRNA] > 1)
fprintf(f,"tRNA GC range = %2.1f%% to %2.1f%%\n",
gcmin[0]*100.0,gcmax[0]*100.0); }}
if (sw->tmrna)
{ sw->ngene[tmRNA] += n[tmRNA];
if ((n[tmRNA] > 1) || (trna && (n[tRNA] > 0)))
fprintf(f,"Number of %s = %d\n",genetype_name[tmRNA],n[tmRNA]); }
sw->nps += nps;
if (sw->reportpseudogenes)
if (nps > 0)
if (n[NS-1] > 1)
fprintf(f,"Number of possible pseudogenes = %d\n",nps);
fputc('\n',f);
fputc('\n',f); }
void batch_energy_stats(data_set *d, int nt, csw *sw)
{ int i,n[NS],genetype,introns,nintron,trna,mtrna,ntv,nd,nps;
double gc,gcmin[NS],gcmax[NS];
FILE *f = sw->f;
mtrna = sw->mtrna;
trna = sw->trna | mtrna;
nps = 0;
if (mtrna)
{ ntv = 0;
nd = 0; }
if ((sw->trna) && (sw->maxintronlen > 0))
{ introns = 1;
nintron = 0; }
else
introns = 0;
for (i = 0; i < NS; i++)
{ n[i] = 0;
gcmin[i] = 1.0;
gcmax[i] = 0.0; }
for (i = 0; i < nt; i++)
if (ts[i].energy >= 0.0)
{ n[NS-1]++;
genetype = ts[i].genetype;
n[genetype]++;
if (ts[i].energy < 100.0) nps++;
if (genetype == tRNA)
{ if (mtrna)
{ if (ts[i].tstem == 0) ntv++;
if (ts[i].dstem == 0) nd++; }
if (introns) if (ts[i].nintron > 0) nintron++;
gc = gc_content(ts+i);
if (gc < gcmin[genetype]) gcmin[genetype] = gc;
if (gc > gcmax[genetype]) gcmax[genetype] = gc; }}
if (trna) sw->ngene[tRNA] += n[tRNA];
if (sw->tmrna) sw->ngene[tmRNA] += n[tmRNA];
sw->nps += nps; }
int gene_sort(data_set *d, int nt, int sort[], csw *sw)
{ int i,n,j,k;
long starti,startj,stopi,stopj,psmax;
psmax = d->psmax;
n = 0;
for (i = 0; i < nt; i++)
if (ts[i].energy >= 0.0)
{ if (sw->ireportminintronlen == 1)
if (ts[i].genetype == tRNA)
if (ts[i].nintron < sw->minintronlenreport)
continue;
sort[n++] = i; }
i = -1;
while (++i < (n-1))
{ j = i;
while (++j < n)
{ starti = ts[sort[i]].start;
startj = ts[sort[j]].start;
stopi = ts[sort[i]].stop;
stopj = ts[sort[j]].stop;
if (stopi < starti)
if ((psmax - starti) < stopi) starti -= psmax;
else stopi += psmax;
if (stopj < startj)
if ((psmax - startj) < stopj) startj -= psmax;
else stopj += psmax;
if (starti > startj)
{ k = sort[i];
sort[i] = sort[j];
sort[j] = k; }
else
if (starti == startj)
if (stopi < stopj)
{ k = sort[i];
sort[i] = sort[j];
sort[j] = k; }}}
return(n); }
int iamatch(data_set *d, gene *t, csw *sw)
{ char key[5],*k,s[100];
if (!(k = softstrpos(d->seqname,"TRNA-"))) return(-1);
copy3cr(k+5,key,3);
name(t,s,1,sw);
if (softstrpos(s,key)) return(1);
return(0); }
int nearest_annotated_gene(data_set *d, gene *t, int matchgenetype)
{ int n,i,nagene,max;
long a,b,c,e,score,thresh,psmax,proximity;
annotated_gene *ta;
psmax = d->psmax;
nagene = d->nagene[NS-1];
ta = d->gene;
n = -1;
max = 0;
proximity = matchgenetype?40:1;
a = t->start;
b = t->stop;
thresh = b-a;
if (b < a)
{ b += psmax;
thresh += psmax;
for (i = 0; i < nagene; i++)
{ c = ta[i].start;
e = ta[i].stop;
if (e < c)
{ e += psmax;
if (a > e) goto NXTW;
if (b < c) goto NXTW;
if (matchgenetype)
if (ta[i].genetype != t->genetype) continue;
score = (a >= c)?((b >= e)?e-a:thresh):((b >= e)?thresh:b-c);
if (score >= proximity)
if (score > max)
{ n = i;
max = score; }
NXTW:
c -= psmax;
e -= psmax; }
if (a > e) continue;
if (b < c) continue;
if (matchgenetype)
if (ta[i].genetype != t->genetype) continue;
score = (a >= c)?((b >= e)?e-a:thresh):((b >= e)?thresh:b-c);
if (score >= proximity)
if (score > max)
{ n = i;
max = score; } }
a -= psmax;
b -= psmax; }
for (i = 0; i < nagene; i++)
{ c = ta[i].start;
e = ta[i].stop;
if (e < c)
{ e += psmax;
if (a > e) goto NXTN;
if (b < c) goto NXTN;
if (matchgenetype)
if (ta[i].genetype != t->genetype) continue;
score = (a >= c)?((b >= e)?e-a:thresh):((b >= e)?thresh:b-c);
if (score >= proximity)
if (score > max)
{ n = i;
max = score; }
NXTN:
c -= psmax;
e -= psmax; }
if (a > e) continue;
if (b < c) continue;
if (matchgenetype)
if (ta[i].genetype != t->genetype) continue;
score = (a >= c)?((b >= e)?e-a:thresh):((b >= e)?thresh:b-c);
if (score >= proximity)
if (score > max)
{ n = i;
max = score; } }
return(n); }
int nearest_detected_gene(data_set *d, int *sort, int ns,
int proxtype, int *overlap,
annotated_gene *t)
{ int n,i,is;
long a,b,c,e,score,thresh,scoremax,psmax;
long proximity;
double energy;
psmax = d->psmax;
n = -1;
energy = -INACTIVE;
scoremax = -1;
a = t->start;
b = t->stop;
thresh = b-a;
proximity = thresh;
if (proximity < 0) proximity = -proximity;
proximity = 1 + proximity/2;
if (proximity > 40) proximity = 40;
if (b < a)
{ b += psmax;
thresh += psmax;
for (i = 0; i < ns; i++)
{ is = sort[i];
c = ts[is].start;
e = ts[is].stop;
if (e < c)
{ e += psmax;
if (a > e) goto NXTW;
if (b < c) goto NXTW;
if (ts[is].genetype != t->genetype) continue;
score = (a >= c)?((b >= e)?e-a:thresh):((b >= e)?thresh:b-c);
if (score >= proximity)
if (proxtype)
{ if (score > scoremax)
{ n = i;
scoremax = score; }}
else
if (ts[is].energy > energy)
{ n = i;
scoremax = score;
energy = ts[is].energy; }
NXTW:
c -= psmax;
e -= psmax; }
if (a > e) continue;
if (b < c) continue;
if (ts[is].genetype != t->genetype) continue;
score = (a >= c)?((b >= e)?e-a:thresh):((b >= e)?thresh:b-c);
if (score >= proximity)
if (proxtype)
{ if (score > scoremax)
{ n = i;
scoremax = score; }}
else
if (ts[is].energy > energy)
{ n = i;
scoremax = score;
energy = ts[is].energy; } }
a -= psmax;
b -= psmax; }
for (i = 0; i < ns; i++)
{ is = sort[i];
c = ts[is].start;
e = ts[is].stop;
if (e < c)
{ e += psmax;
if (a > e) goto NXTN;
if (b < c) goto NXTN;
if (ts[is].genetype != t->genetype) continue;
score = (a >= c)?((b >= e)?e-a:thresh):((b >= e)?thresh:b-c);
if (score >= proximity)
if (proxtype)
{ if (score > scoremax)
{ n = i;
scoremax = score; }}
else
if (ts[is].energy > energy)
{ n = i;
scoremax = score;
energy = ts[is].energy; }
NXTN:
c -= psmax;
e -= psmax; }
if (a > e) continue;
if (b < c) continue;
if (ts[is].genetype != t->genetype) continue;
score = (a >= c)?((b >= e)?e-a:thresh):((b >= e)?thresh:b-c);
if (score >= proximity)
if (proxtype)
{ if (score > scoremax)
{ n = i;
scoremax = score; }}
else
if (ts[is].energy > energy)
{ n = i;
scoremax = score;
energy = ts[is].energy; } }
*overlap = (scoremax + 1);
return(n); }
void disp_match(data_set *d, int *sort, int nd, csw *sw)
{ int i,ld,fn,fp,fpd,fptv,w,alen,overlap,length,detect[NGFT],n[NS];
char nm[100],anm[100],ps[100],*s;
FILE *f = sw->f;
gene *t;
annotated_gene *agene;
static char comp[3] = " c";
for (i = 0; i < NS; i++) n[i] = 0;
for (i = 0; i < nd; i++)
{ w = sort[i];
if (ts[w].energy >= 0.0)
{ n[NS-1]++;
n[ts[w].genetype]++; }}
fprintf(f,"\n%s\n",d->seqname);
fprintf(f,"%ld nucleotides in sequence\n",d->psmax);
fprintf(f,"Mean G+C content = %2.1f%%\n",100.0*d->gc);
fprintf(f,"GenBank to Aragorn Comparison\n");
if (sw->trna | sw->mtrna)
{ fn = 0;
fp = 0;
fpd = 0;
fptv = 0;
fprintf(f,"\n%d annotated tRNA genes\n",d->nagene[tRNA]);
fprintf(f,"%d detected tRNA genes\n\n",n[tRNA]);
fprintf(f," GenBank\t\t\t\tAragorn\n");
ld = 0;
for (i = 0; i < d->nagene[NS-1]; i++)
{ agene = d->gene + i;
if (agene->genetype != tRNA) continue;
detect[i] = nearest_detected_gene(d,sort,nd,0,&overlap,agene);
while (ld < nd)
{ t = ts + sort[ld];
if (detect[i] >= 0)
if (ld >= detect[i]) break;
if (t->start < t->stop)
if (t->start > agene->start) break;
fprintf(f,"* Not annotated %s ",name(t,nm,1,sw));
fprintf(f,"%s",position(ps,t,sw));
if (sw->reportpseudogenes)
if (pseudogene(t))
fprintf(f," PS");
fputc('\n',f);
fp++;
if (t->genetype == tRNA)
{ if (t->dstem == 0) fpd++;
if (t->tstem == 0) fptv++; }
ld++; }
if (detect[i] >= 0)
{ ld = detect[i] + 1;
w = 0;
t = ts + sort[detect[i]];
s = aa(t->seq + t->anticodon,sw);
if (!softstrpos(s,agene->species+5)) w += 1;
if (agene->comp != t->comp) w += 2;
alen = agene->stop - agene->start;
if (alen < 0) alen = -alen;
if (alen < (t->nbase - 10)) w += 4;
else if (alen > (t->nbase + 10)) w += 4;
if (w > 0) fputc('*',f);
else fputc(' ',f); }
else
fputc('*',f);
sprintf(anm," %s %c(%ld,%ld)",
agene->species,comp[agene->comp],agene->start,agene->stop);
fprintf(f,"%-30s ",anm);
if (detect[i] >= 0)
{ fprintf(f,"%s ",name(t,nm,1,sw));
fprintf(f,"%s",position(ps,t,sw));
if (sw->reportpseudogenes)
if (pseudogene(t))
fprintf(f," PS");
if (w & 1) fprintf(f," AAM");
if (w & 2) fprintf(f," SM");
if (w & 4) fprintf(f," LM");
fputc('\n',f); }
else
{ fprintf(f,"Not detected\n");
fn++; }}
while (ld < nd)
{ fprintf(f,"* Not annotated\t\t\t%s ",name(ts + sort[ld],nm,1,sw));
fprintf(f,"%s\n",position(ps,ts + sort[ld],sw));
fp++;
if (t->genetype == tRNA)
{ if (t->dstem == 0) fpd++;
if (t->tstem == 0) fptv++; }
ld++; }
fprintf(f,"\nNumber of false negative genes = %d\n",fn);
fprintf(f,"Number of false positive genes = %d\n",fp);
fprintf(f,"Number of false positive D-replacement tRNA genes = %d\n",fpd);
fprintf(f,"Number of false positive TV-replacement tRNA genes = %d\n",fptv);
fprintf(f,"\n\n");
sw->nagene[tRNA] += d->nagene[tRNA];
sw->natfn += fn;
sw->natfp += fp;
sw->natfpd += fpd;
sw->natfptv += fptv; }
if (sw->cds)
{ fn = 0;
fp = 0;
fprintf(f,"\n%d annotated CDS genes\n",d->nagene[CDS]);
fprintf(f,"%d detected CDS genes\n\n",n[CDS]);
fprintf(f," GenBank\t\t\t\t Aragorn\n");
ld = 0;
for (i = 0; i < d->nagene[NS-1]; i++)
{ agene = d->gene + i;
if (agene->genetype != CDS) continue;
length = (int)(agene->stop - agene->start) + 1;
sw->lacds += length;
detect[i] = nearest_detected_gene(d,sort,nd,1,&overlap,agene);
while (ld < nd)
{ t = ts + sort[ld];
if (detect[i] >= 0)
if (ld >= detect[i]) break;
if (t->start < t->stop)
if (t->start > agene->start) break;
fprintf(f,"* Not annotated ");
sprintf(anm,"%s %s",
name(t,nm,1,sw),position(ps,t,sw));
fprintf(f,"%-18s",anm);
if (sw->energydisp) fprintf(f," %lg",t->energy);
if (sw->reportpseudogenes)
if (pseudogene(t))
fprintf(f," PS");
fputc('\n',f);
fp++;
ld++; }
if (detect[i] >= 0)
{ ld = detect[i] + 1;
t = ts + sort[detect[i]];
fputc(' ',f); }
else
fputc('*',f);
fprintf(f," %-33s",agene->species);
sprintf(anm,"%c(%ld,%ld)",comp[agene->comp],agene->start,agene->stop);
fprintf(f,"%14s ",anm);
if (detect[i] >= 0)
{ sprintf(anm,"%s %s",name(t,nm,1,sw),position(ps,t,sw));
fprintf(f,"%-18s",anm);
if (sw->energydisp) fprintf(f," %lg",t->energy);
if (sw->reportpseudogenes)
if (pseudogene(t))
fprintf(f," PS");
fputc('\n',f);
length = (int)(t->stop - t->start) + 1;
sw->ldcds += length; }
else
{ fprintf(f,"Not detected\n");
fn++; }}
while (ld < nd)
{ t = ts + sort[ld];
fprintf(f,"* Not annotated ");
sprintf(anm,"%s %s",name(t,nm,1,sw),position(ps,t,sw));
fprintf(f,"%-18s",anm);
if (sw->energydisp) fprintf(f," %lg",t->energy);
if (sw->reportpseudogenes)
if (pseudogene(t))
fprintf(f," PS");
fputc('\n',f);
fp++;
ld++; }
fprintf(f,"\nNumber of false negative CDS genes = %d\n",fn);
fprintf(f,"Number of false positive CDS genes = %d\n",fp);
fprintf(f,"\n\n");
sw->nagene[CDS] += d->nagene[CDS];
sw->nacdsfn += fn;
sw->nacdsfp += fp; }
sw->nabase += d->psmax; }
void disp_gene_set(data_set *d, int nt, csw *sw)
{ int i,j,n,a,vsort[NT],*sort;
char m[MATX][MATY],s[20];
static char comp[3] = " c";
gene *t;
FILE *f = sw->f;
if (nt <= NT)
sort = vsort;
else
{ sort = (int *)malloc(nt*sizeof(int));
if (sort == NULL)
{ fprintf(stderr,"Not enough memory to sort genes\n");
exit(1); }}
n = gene_sort(d,nt,sort,sw);
j = sw->tmrna_struct[54];
for (i = 55; i <= 60; i++) j += sw->tmrna_struct[i];
if (j != ((sw->tmrna_struct[0] << 4) + 9)) return;
if (sw->libflag < 2)
{ if (n > 0)
for (j = 0; j < n;)
{ i = sort[j++];
t = ts + i;
t->energy = nenergy(t,sw);
switch(t->genetype)
{ case tRNA:
init_matrix(m);
disp_gene(t,m,sw);
sprintf(s,"%d.",j);
xcopy(m,0,32,s,length(s));
disp_matrix(f,m,MATY);
if (sw->matchacceptor)
if (iamatch(d,t,sw) == 0)
{ fprintf(f," Iso-acceptor mismatch\n");
sw->iamismatch++; }
if (sw->annotated)
if ((a = nearest_annotated_gene(d,t,1)) < 0)
{ fprintf(f," Annotation false positive\n");
if ((a = nearest_annotated_gene(d,t,0)) >= 0)
fprintf(f," Overlap with %s %c(%ld,%ld)\n",
d->gene[a].species,comp[d->gene[a].comp],
d->gene[a].start,d->gene[a].stop);
fputc('\n',f); }
overlap(d,sort,n,i,sw);
if (sw->seqdisp) disp_seq(f,t,sw);
if (t->nintron > 0) disp_intron(f,t,sw);
if (sw->energydisp > 1) trna_score(f,t);
break;
case tmRNA:
if (sw->secstructdisp == 1)
{ init_matrix(m);
disp_gene(t,m,sw);
sprintf(s,"%d.",j);
xcopy(m,0,32,s,length(s));
disp_matrix(f,m,MATY); }
else
{ fprintf(f,"\n%d.\n",j);
disp_location(t,sw,"Location");
if (sw->energydisp)
fprintf(f,"Score = %g\n",t->energy); }
overlap(d,sort,n,i,sw);
if (t->asst == 0) disp_tmrna_seq(f,t,sw);
else disp_tmrna_perm_seq(f,t,sw);
if (sw->energydisp > 1) tmrna_score(f,t,sw);
break;
case CDS:
fprintf(f,"\n%d.\nCDS gene\n",j);
disp_location(t,sw,"Location");
overlap(d,sort,n,i,sw);
disp_cds(f,t,sw);
break;
}
if (sw->libflag > 0) write_to_library(f,t,sw); }
else
if (*(d->seqname) != '\0')
fprintf(f,"\nNothing found in %s\n\n\n",d->seqname);
else
fprintf(f,"\nNothing found\n\n\n"); }
else
{ if (n > 0)
for (i = 0; i < n; i++)
write_to_library(f,ts + sort[i],sw); }
disp_energy_stats(d,nt,sw);
if (d->datatype == GENBANK) disp_match(d,sort,n,sw);
if (nt > NT) free((void *)sort); }
void batch_gene_set(data_set *d, int nt, csw *sw)
{ int i,j,n,vsort[NT],nspaces,caps,*sort;
gene *t;
FILE *f = sw->f;
if (nt <= NT)
sort = vsort;
else
{ sort = (int *)malloc(nt*sizeof(int));
if (sort == NULL)
{ fprintf(stderr,"Not enough memory to sort genes\n");
exit(1); }}
n = gene_sort(d,nt,sort,sw);
j = sw->tmrna_struct[54];
for (i = 55; i <= 60; i++) j += sw->tmrna_struct[i];
if (j != ((sw->tmrna_struct[0] << 4) + 9)) return;
if (sw->libflag < 2)
if (sw->batch >= 2)
{ nspaces = (sw->batch & 0x4);
caps = (sw->batch & 0x10);
if (sw->batch & 0x8)
for (i = 0; i < n; i++)
disp_fasta_seq(f,ts + sort[i],d->ns+1,i+1,nspaces,caps,sw);
else
for (i = 0; i < n; i++)
disp_fasta_seq(f,ts + sort[i],0,0,nspaces,caps,sw); }
else
{ fprintf(f,"%d genes found\n",n);
for (j = 0; j < n; j++)
{ fprintf(f,"%-3d ",j+1);
t = ts + sort[j];
t->energy = nenergy(t,sw);
switch(t->genetype)
{ case tRNA: disp_batch_trna(f,t,sw);
break;
case tmRNA: disp_batch_tmrna(f,t,sw);
break;
case srpRNA:disp_batch_srprna(f,t,sw);
break;
case CDS: disp_batch_cds(f,t,sw);
break;
default: break; }}}
if (sw->libflag > 0)
{ for (i = 0; i < n; i++)
write_to_library(f,ts + sort[i],sw); }
batch_energy_stats(d,nt,sw);
if (nt > NT) free((void *)sort); }
void remove_overlapping_trna(data_set *d, int nt, csw *sw)
{ int i,n,ioverlay;
long a,b,c,e,len,leni,overlap,psmax;
char s1[80],s2[80];
gene *t,*ti;
static long proximity = 7*MINCTRNALEN/10;
psmax = d->psmax;
ioverlay = sw->ioverlay;
for (n = 0; n < nt; n++)
{ t = ts + n;
if (t->genetype != tRNA) continue;
if (t->energy < 0.0) continue;
if (t->nintron <= 0) continue;
a = t->start;
b = t->stop;
if (b < a) b += psmax;
len = b - a;
for (i = 0; i < nt; i++)
{ if (i == n) continue;
ti = ts + i;
if (ti->genetype != tRNA) continue;
if (ti->comp != t->comp) continue;
if (ti->energy < 0.0) continue;
c = ti->start;
e = ti->stop;
if (e < c) e += psmax;
leni = e - c;
if (ioverlay)
{ if ((2*len) > (5*leni)) continue;
if ((2*leni) > (5*len)) continue; }
overlap = (a >= c)?((b >= e)?e-a:len):((b >= e)?len:b-c);
if (overlap >= proximity)
if (t->energy < ti->energy)
{ if (sw->verbose)
{ fprintf(stderr,"Removing %s at %s",name(t,s1,0,sw),position(s2,t,sw));
if (sw->energydisp) fprintf(stderr," (%g)",nenergy(t,sw));
fprintf(stderr,"\n"); }
t->energy = -1.0;
break; }}}
for (n = 0; n < (nt-1); n++)
{ t = ts + n;
if (t->genetype != tRNA) continue;
if (t->energy < 0.0) continue;
a = t->start;
b = t->stop;
if (b < a) b += psmax;
len = b - a;
for (i = n + 1; i < nt; i++)
{ ti = ts + i;
if (ti->genetype != tRNA) continue;
if (ti->comp != t->comp) continue;
if (ti->energy < 0.0) continue;
c = ti->start;
e = ti->stop;
if (e < c) e += psmax;
leni = e - c;
if (ioverlay)
{ if ((2*len) > (5*leni)) continue;
if ((2*leni) > (5*len)) continue; }
overlap = (a >= c)?((b >= e)?e-a:len):((b >= e)?len:b-c);
if (overlap >= proximity)
if (t->energy < ti->energy)
{ if (sw->verbose)
{ fprintf(stderr,"Removing %s at %s",name(t,s1,0,sw),position(s2,t,sw));
if (sw->energydisp) fprintf(stderr," (%g)",nenergy(t,sw));
fprintf(stderr,"\n"); }
t->energy = -1.0;
break; }
else if (ti->energy < t->energy)
{ if (sw->verbose)
{ fprintf(stderr,"Removing %s at %s",name(ti,s1,0,sw),position(s2,ti,sw));
if (sw->energydisp) fprintf(stderr," (%g)",nenergy(ti,sw));
fprintf(stderr,"\n"); }
ti->energy = -1.0; }}}}
void iopt_fastafile(data_set *d, csw *sw)
{ int i,nt,flag,len,aragorn,anticodon;
int *s,*sf,*se,*sc,*swrap;
int seq[2*LSEQ+WRAP+1],cseq[2*LSEQ+WRAP+1],wseq[2*WRAP+1];
long gap,start,rewind,drewind,psmax,tmaxlen,vstart,vstop;
double sensitivity,sel1,sel2;
char c1,c2,c3;
static char trnatypename[3][25] =
{ "Metazoan mitochondrial","Cytosolic","Mammalian mitochondrial" };
static char genecodename[NGENECODE][50] =
{ "composite Metazoan Mitochondrial",
"standard",
"Vertebrate Mitochondrial",
"Yeast Mitochondrial",
"Mold/Protozoan/Coelenterate Mitochondrial",
"Invertebrate Mitochondrial",
"Ciliate",
"deleted -> standard",
"deleted -> standard",
"Echinoderm/Flatworm Mitochondrial",
"Euplotid",
"Bacterial/Plant Chloroplast",
"Alternative Yeast",
"Ascidian Mitochondrial",
"Alternative Flatworm Mitochondrial",
"Blepharisma",
"Chlorophycean Mitochondrial",
"deleted -> standard",
"deleted -> standard",
"deleted -> standard",
"deleted -> standard",
"Trematode Mitochondrial",
"Scenedesmus obliquus Mitochondrial",
"Thraustochytrium Mitochondrial" };
FILE *f = sw->f;
init_tmrna(f,sw);
aragorn = (sw->trna || sw->tmrna || sw->cds || sw->srprna);
fprintf(f,"\nPlease reference the following paper");
if (aragorn && sw->mtrna) fputc('s',f);
fprintf(f," if you use this\n");
fprintf(f,"program as part of any published research.\n\n");
if (aragorn)
{ fprintf(f,"Laslett, D. and Canback, B. (2004) ARAGORN, a\n");
fprintf(f,"program for the detection of transfer RNA and\n");
fprintf(f,"transfer-messenger RNA genes in nucleotide sequences.\n");
fprintf(f,"Nucleic Acids Research, 32;11-16.\n\n"); }
if (sw->mtrna)
{ fprintf(f,"Laslett, D. and Canback, B. (2008) ARWEN: a\n");
fprintf(f,"program to detect tRNA genes in metazoan mitochondrial\n");
fprintf(f,"nucleotide sequences\n");
fprintf(f,"Bioinformatics, 24(2); 172-175.\n\n\n"); }
fputc('\n',f);
if (sw->mtrna)
{ fprintf(f,"Searching for %s tRNA genes\n",trnatypename[sw->discrim]);
if (!sw->tvloop)
fprintf(f,"TV replacement loop tRNA genes not detected\n"); }
else
if (sw->trna)
{ fprintf(f,"Searching for tRNA genes");
if (sw->maxintronlen > 0) fprintf(f," with introns in anticodon loop");
else fprintf(f," with no introns");
fputc('\n',f);
if (sw->maxintronlen > 0)
{ fprintf(f,"Intron length from %d to %d bases\n",
sw->minintronlen,sw->maxintronlen);
if (sw->ifixedpos)
{ fprintf(f,"Intron position fixed between positions 37 and 38\n");
fprintf(f,"on C-loop (one base after anticodon)\n"); }
if (sw->ioverlay)
fprintf(f,"Allowing overlay of long tRNA genes\n"); }}
if (sw->tmrna)
fprintf(f,"Searching for tmRNA genes\n");
if (sw->linear)
fprintf(f,"Assuming linear topology, search will not wrap around ends\n");
else
fprintf(f,"Assuming circular topology, search wraps around ends\n");
if (sw->both == 2)
fprintf(f,"Searching both strands\n");
else
if (sw->both == 1)
fprintf(f,"Searching complementary (antisense) strand only\n");
else
fprintf(f,"Searching single (sense) strand only\n");
if (sw->mtrna)
if (sw->mtcompov)
fprintf(f,"Reporting overlapping candidates on opposite strands\n");
if ((sw->mtrna) || (sw->trna) || (sw->tmrna))
{ fprintf(f,"Using %s genetic code\n",genecodename[sw->geneticcode]);
if (sw->ngcmod > 0)
{ fprintf(f,"Specified modifications:\n");
for (i = 0; i < sw->ngcmod; i++)
{ anticodon = sw->gcmod[i];
c1 = cpbase(Thymine - (anticodon & 0x3));
c2 = cpbase(Thymine - ((anticodon >> 2) & 0x3));
c3 = cpbase(Thymine - ((anticodon >> 4) & 0x3));
fprintf(f,"%c%c%c = %s\n",c1,c2,c3,
aaname[aamap[sw->geneticcode][anticodon]]); }}}
fputc('\n',f);
fputc('\n',f);
rewind = MAXTAGDIST + 20;
if (sw->trna | sw->mtrna)
{ tmaxlen = MAXTRNALEN + sw->maxintronlen;
if (rewind < tmaxlen) rewind = tmaxlen; }
if (sw->tmrna)
if (rewind < MAXTMRNALEN) rewind = MAXTMRNALEN;
if (sw->peptide)
if (sw->tagthresh >= 5)
if (rewind < TSWEEP) rewind = TSWEEP;
sw->loffset = rewind;
sw->roffset = rewind;
drewind = 2*rewind;
d->ns = 0;
d->nextseq = 0L;
while (d->nextseq >= 0L)
{ d->seqstart = d->nextseq;
if (!seq_init(d,sw)) break;
psmax = d->psmax;
if (sw->verbose)
{ fprintf(stderr,"%s\n",d->seqname);
fprintf(stderr,"%ld nucleotides in sequence\n",psmax);
fprintf(stderr,"Mean G+C content = %2.1f%%\n",100.0*d->gc);
if ((sw->mtrna) || (sw->trna) || (sw->tmrna))
{ fprintf(stderr,"Using %s genetic code\n",genecodename[sw->geneticcode]);
if (sw->ngcmod > 0)
{ fprintf(stderr,"Specified modifications:\n");
for (i = 0; i < sw->ngcmod; i++)
{ anticodon = sw->gcmod[i];
c1 = cpbase(Thymine - (anticodon & 0x3));
c2 = cpbase(Thymine - ((anticodon >> 2) & 0x3));
c3 = cpbase(Thymine - ((anticodon >> 4) & 0x3));
fprintf(stderr,"%c%c%c = %s\n",c1,c2,c3,
aaname[aamap[sw->geneticcode][anticodon]]); }}}}
fprintf(f,"%s\n",d->seqname);
fprintf(f,"%ld nucleotides in sequence\n",psmax);
fprintf(f,"Mean G+C content = %2.1f%%\n",100.0*d->gc);
init_gene(0,NT);
nt = 0;
flag = 0;
start = 1L;
se = seq;
if (sw->linear)
{ for (i = 0; i < rewind; i++) *se++ = NOBASE;
start -= rewind; }
else
{ if (psmax <= drewind)
{ gap = drewind - psmax;
sc = se + gap;
while (se < sc) *se++ = NOBASE;
swrap = wseq;
sc = se + psmax;
while (se < sc)
{ *se = move_forward(d);
*swrap++ = *se++; }
sc = swrap + gap;
while (swrap < sc) *swrap++ = NOBASE;
swrap = wseq;
sc = swrap + psmax;
while (swrap < sc) *se++ = *swrap++;
swrap = wseq;
sc = swrap + drewind;
while (swrap < sc) *se++ = *swrap++;
sw->loffset = drewind;
sw->roffset = drewind;
start -= drewind;
flag = 1;
goto SH; }
else
{ swrap = wseq;
sc = seq + drewind;
while (se < sc)
{ *se = move_forward(d);
*swrap++ = *se++; }}}
sc = seq + LSEQ;
NX:
while (se < sc)
{ if (d->ps >= psmax)
{ if (sw->linear)
for (i = 0; i < rewind; i++) *se++ = NOBASE;
else
{ sc = wseq + drewind;
swrap = wseq;
while (swrap < sc) *se++ = *swrap++; }
flag = 1;
break; }
else *se++ = move_forward(d); }
SH:
len = (int)(se - seq);
if (sw->verbose)
{ vstart = sq(start + sw->loffset);
vstop = sq(start + len - sw->roffset - 1);
if (vstop < vstart)
{ fprintf(stderr,"Searching from %ld to %ld\n",vstart,psmax);
fprintf(stderr,"Searching from 1 to %ld\n",vstop); }
else
fprintf(stderr,"Searching from %ld to %ld\n",vstart,vstop); }
if (sw->both != 1)
{ sw->start = start;
sw->comp = 0;
nt = tmioptimise(d,seq,len,nt,sw); }
if (sw->both > 0)
{ sense_switch(seq,cseq,len);
sw->start = start+len;
sw->comp = 1;
nt = tmioptimise(d,cseq,len,nt,sw); }
if (!flag)
{ s = seq;
sf = se - drewind;
se = seq + drewind;
while (s < se) *s++ = *sf++;
start += len - drewind;
goto NX; }
if (sw->maxintronlen > 0) remove_overlapping_trna(d,nt,sw);
disp_gene_set(d,nt,sw);
if (sw->verbose) fprintf(stderr,"%s\nSearch Finished\n\n",d->seqname);
d->ns++; }
if (d->ns > 1)
{ fprintf(f,"\n\n%d sequences searched\n",d->ns);
if (sw->trna | sw->mtrna)
{ fprintf(f,"Total tRNA genes = %d\n",sw->ngene[tRNA]);
if (sw->matchacceptor)
fprintf(f,"Total iso-acceptor mismatches = %d\n",sw->iamismatch); }
if (sw->tmrna) fprintf(f,"Total tmRNA genes = %d\n",sw->ngene[tmRNA]);
if (sw->reportpseudogenes)
if (sw->nps > 0)
fprintf(f,"Total number of possible pseudogenes = %d\n",sw->nps);
if (sw->annotated)
{ if (sw->trna | sw->mtrna)
{ fprintf(f,"\nTotal number of annotated tRNA genes = %d\n",
sw->nagene[tRNA]);
fprintf(f,"Total number of annotated false negatives = %d\n",sw->natfn);
fprintf(f,"Total number of annotated false positives = %d\n",sw->natfp);
fprintf(f,"Total number of annotated DRL false positives = %d\n",
sw->natfpd);
fprintf(f,"Total number of annotated TVRL false positives = %d\n",
sw->natfptv);
fprintf(f,"Total annotated sequence length = %ld bases\n",sw->nabase);
sensitivity = (sw->nagene[tRNA] > 0)?
100.0*(double)(sw->nagene[tRNA] - sw->natfn)/
(double)sw->nagene[tRNA]:0.0;
sel1 = (sw->nagene[tRNA] > 0)?
100.0*(double)(sw->natfp)/
(double)sw->nagene[tRNA]:0.0;
sel2 = (sw->nabase > 0)?
1000000.0*(double)(sw->natfp)/
(double)sw->nabase:0.0;
fprintf(f,"Sensitivity = %lg%%\n",sensitivity);
fprintf(f,"Selectivity = %lg%% or %lg per Megabase\n\n",sel1,sel2); }
if (sw->cds)
{ fprintf(f,"\nTotal number of annotated CDS genes = %d\n",
sw->nagene[CDS]);
fprintf(f,"Total number of annotated false negatives = %d\n",sw->nacdsfn);
fprintf(f,"Total number of annotated false positives = %d\n",sw->nacdsfp);
fprintf(f,"Total annotated sequence length = %ld bases\n",sw->nabase);
sensitivity = (sw->nagene[CDS] > 0)?
100.0*(double)(sw->nagene[CDS] - sw->nacdsfn)/
(double)sw->nagene[CDS]:0.0;
sel1 = (sw->nagene[CDS] > 0)?
100.0*(double)(sw->nacdsfp)/
(double)sw->nagene[CDS]:0.0;
sel2 = (sw->nabase > 0)?
1000000.0*(double)(sw->nacdsfp)/
(double)sw->nabase:0.0;
fprintf(f,"Sensitivity = %lg%%\n",sensitivity);
fprintf(f,"Selectivity = %lg%% or %lg per Megabase\n",sel1,sel2);
sensitivity = (sw->lacds > 0)?
100.0*(double)sw->ldcds/(double)sw->lacds:0.0;
fprintf(f,"Length sensitivity = %lg%%\n\n",sensitivity); }
} }
}
void bopt_fastafile(data_set *d, csw *sw)
{ int i,nt,flag,len;
int *s,*sf,*se,*sc,*swrap;
int seq[2*LSEQ+WRAP+1],cseq[2*LSEQ+WRAP+1],wseq[2*WRAP+1];
long gap,start,rewind,drewind,psmax,tmaxlen,vstart,vstop;
FILE *f = sw->f;
rewind = MAXTAGDIST + 20;
if (sw->trna | sw->mtrna)
{ tmaxlen = MAXTRNALEN + sw->maxintronlen;
if (rewind < tmaxlen) rewind = tmaxlen; }
if (sw->tmrna)
if (rewind < MAXTMRNALEN) rewind = MAXTMRNALEN;
if (sw->peptide)
if (sw->tagthresh >= 5)
if (rewind < TSWEEP) rewind = TSWEEP;
sw->loffset = rewind;
sw->roffset = rewind;
drewind = 2*rewind;
d->ns = 0;
d->nextseq = 0L;
while (d->nextseq >= 0L)
{ d->seqstart = d->nextseq;
if (!seq_init(d,sw)) break;
psmax = d->psmax;
if (sw->verbose)
{ fprintf(stderr,"%s\n",d->seqname);
fprintf(stderr,"%ld nucleotides in sequence\n",psmax);
fprintf(stderr,"Mean G+C content = %2.1f%%\n",100.0*d->gc); }
if (sw->batch < 2) fprintf(f,">%s\n",d->seqname);
init_gene(0,NT);
nt = 0;
flag = 0;
start = 1L;
se = seq;
if (sw->linear)
{ for (i = 0; i < rewind; i++) *se++ = NOBASE;
start -= rewind; }
else
{ if (psmax <= drewind)
{ gap = drewind - psmax;
sc = se + gap;
while (se < sc) *se++ = NOBASE;
swrap = wseq;
sc = se + psmax;
while (se < sc)
{ *se = move_forward(d);
*swrap++ = *se++; }
sc = swrap + gap;
while (swrap < sc) *swrap++ = NOBASE;
swrap = wseq;
sc = swrap + psmax;
while (swrap < sc) *se++ = *swrap++;
swrap = wseq;
sc = swrap + drewind;
while (swrap < sc) *se++ = *swrap++;
sw->loffset = drewind;
sw->roffset = drewind;
start -= drewind;
flag = 1;
goto SH; }
else
{ swrap = wseq;
sc = seq + drewind;
while (se < sc)
{ *se = move_forward(d);
*swrap++ = *se++; }}}
sc = seq + LSEQ;
NX:
while (se < sc)
{ *se++ = move_forward(d);
if (d->ps >= psmax)
{ if (sw->linear)
for (i = 0; i < rewind; i++) *se++ = NOBASE;
else
{ sc = wseq + drewind;
swrap = wseq;
while (swrap < sc) *se++ = *swrap++; }
flag = 1;
break; }}
SH:
len = (int)(se - seq);
if (sw->verbose)
{ vstart = sq(start + sw->loffset);
vstop = sq(start + len - sw->roffset - 1);
if (vstop < vstart)
{ fprintf(stderr,"Searching from %ld to %ld\n",vstart,psmax);
fprintf(stderr,"Searching from 1 to %ld\n",vstop); }
else
fprintf(stderr,"Searching from %ld to %ld\n",vstart,vstop); }
if (sw->both != 1)
{ sw->start = start;
sw->comp = 0;
nt = tmioptimise(d,seq,len,nt,sw); }
if (sw->both > 0)
{ sense_switch(seq,cseq,len);
sw->start = start+len;
sw->comp = 1;
nt = tmioptimise(d,cseq,len,nt,sw); }
if (!flag)
{ s = seq;
sf = se - drewind;
se = seq + drewind;
while (s < se) *s++ = *sf++;
start += len - drewind;
goto NX; }
if (sw->maxintronlen > 0) remove_overlapping_trna(d,nt,sw);
batch_gene_set(d,nt,sw);
if (sw->verbose) fprintf(stderr,"%s\nSearch Finished\n\n",d->seqname);
d->ns++; }
if ((d->ns > 1) && (sw->batch < 2))
{ fprintf(f,">end \t%d sequences",d->ns);
if (sw->trna || sw->mtrna) fprintf(f," %d tRNA genes",sw->ngene[tRNA]);
if (sw->tmrna) fprintf(f," %d tmRNA genes",sw->ngene[tmRNA]);
fputc('\n',f); } }
void aragorn_help_menu()
{ printf("\n");
printf("----------------------------\n");
printf("ARAGORN v1.2.36 Dean Laslett\n");
printf("----------------------------\n");
printf("\n");
printf("Please reference the following papers if you use this\n");
printf("program as part of any published research.\n\n");
printf("Laslett, D. and Canback, B. (2004) ARAGORN, a\n");
printf("program for the detection of transfer RNA and transfer-messenger\n");
printf("RNA genes in nucleotide sequences\n");
printf("Nucleic Acids Research, 32;11-16\n\n");
printf("Laslett, D. and Canback, B. (2008) ARWEN: a\n");
printf("program to detect tRNA genes in metazoan mitochondrial\n");
printf("nucleotide sequences\n");
printf("Bioinformatics, 24(2); 172-175.\n\n\n");
printf("ARAGORN detects tRNA, mtRNA, and tmRNA genes.\n");
printf("\n");
printf("Usage:\n");
printf("aragorn -v -s -d -c -l -a -w -j -ifro, -t -mt -m");
printf(" -tv -gc -seq -br -fasta -fo -o \n\n");
printf(" is assumed to contain one or more sequences\n");
printf("in FASTA format. Results of the search are printed to\n");
printf("STDOUT. All switches are optional and case-insensitive.\n");
printf("Unless -i is specified, tRNA genes containing introns\n");
printf("are not detected. \n");
printf("\n");
printf(" -m Search for tmRNA genes.\n");
printf(" -t Search for tRNA genes.\n");
printf(" By default, both are detected. If one of\n");
printf(" -m or -t is specified, then the other\n");
printf(" is not detected unless specified as well.\n");
printf(" -mt Search for Metazoan mitochondrial tRNA\n");
printf(" genes. -i switch ignored. Composite\n");
printf(" Metazoan mitochondrial genetic code used.\n");
printf(" -mtmam Search for Mammalian mitochondrial tRNA\n");
printf(" genes. -i switch ignored. -tv switch set.\n");
printf(" Mammalian mitochondrial genetic code used.\n");
printf(" -mtx Same as -mt but low scoring tRNA genes are\n");
printf(" not reported.\n");
printf(" -gc Use the GenBank transl_table = genetic code.\n");
printf(" -gcstd Use standard genetic code.\n");
printf(" -gcmet Use composite Metazoan mitochondrial genetic code.\n");
printf(" -gcvert Use Vertebrate mitochondrial genetic code.\n");
printf(" -gcinvert Use Invertebrate mitochondrial genetic code.\n");
printf(" -gcyeast Use Yeast mitochondrial genetic code.\n");
printf(" -gcprot Use Mold/Protozoan/Coelenterate");
printf(" mitochondrial genetic code.\n");
printf(" -gcciliate Use Ciliate genetic code.\n");
printf(" -gcflatworm Use Echinoderm/Flatworm mitochondrial genetic code.\n");
printf(" -gceuplot Use Euplotid genetic code.\n");
printf(" -gcbact Use Bacterial/Plant Chloroplast genetic code.\n");
printf(" -gcaltyeast Use alternative Yeast genetic code.\n");
printf(" -gcascid Use Ascidian Mitochondrial genetic code.\n");
printf(" -gcaltflat Use alternative Flatworm Mitochondrial genetic code.\n");
printf(" -gcblep Use Blepharisma genetic code.\n");
printf(" -gcchloroph Use Chlorophycean Mitochondrial genetic code.\n");
printf(" -gctrem Use Trematode Mitochondrial genetic code.\n");
printf(" -gcscen Use Scenedesmus obliquus Mitochondrial genetic code.\n");
printf(" -gcthraust Use Thraustochytrium Mitochondrial genetic code.\n");
printf(" Individual modifications can be appended using\n");
printf(" ,BBB= B = A,C,G, or T. is the three letter\n");
printf(" code for an amino-acid. More than one modification\n");
printf(" can be specified. eg -gcvert,aga=Trp,agg=Trp uses\n");
printf(" the Vertebrate Mitochondrial code and the codons\n");
printf(" AGA and AGG changed to Tryptophan.\n");
printf(" -tv Do not search for mitochondrial ");
printf("TV replacement\n");
printf(" loop tRNA genes. Only relevant if -mt used. \n");
printf(" -i Search for tRNA genes with introns in\n");
printf(" anticodon loop with maximum length %d\n",
MAXINTRONLEN);
printf(" bases. Minimum intron length is 0 bases.\n");
printf(" Ignored if -m is specified.\n");
printf(" -i Search for tRNA genes with introns in\n");
printf(" anticodon loop with maximum length \n");
printf(" bases. Minimum intron length is 0 bases.\n");
printf(" Ignored if -m is specified.\n");
printf(" -i, Search for tRNA genes with introns in\n");
printf(" anticodon loop with maximum length \n");
printf(" bases, and minimum length bases.\n");
printf(" Ignored if -m is specified.\n");
printf(" -io Same as -i, but allow tRNA genes with long\n");
printf(" introns to overlap shorter tRNA genes.\n");
printf(" -if Same as -i, but fix intron between positions\n");
printf(" 37 and 38 on C-loop (one base after anticodon).\n");
printf(" -ifo Same as -if and -io combined.\n");
printf(" -ir Same as -i, but search for tRNA genes with minimum intron\n");
printf(" length 0 bases, and only report tRNA genes with minimum\n");
printf(" intron length bases.\n");
printf(" -c Assume that each sequence has a circular\n");
printf(" topology. Search wraps around each end.\n");
printf(" Default setting.\n");
printf(" -l Assume that each sequence has a linear\n");
printf(" topology. Search does not wrap.\n");
printf(" -d Double. Search both strands of each\n");
printf(" sequence. Default setting.\n");
printf(" -s or -s+ Single. Do not search the complementary\n");
printf(" (antisense) strand of each sequence.\n");
printf(" -sc or -s- Single complementary. Do not search the sense\n");
printf(" strand of each sequence.\n");
printf(" -ss Use the stricter canonical 1-2 bp spacer1 and\n");
printf(" 1 bp spacer2. Ignored if -mt set. Default is to\n");
printf(" allow 3 bp spacer1 and 0-2 bp spacer2, which may\n");
printf(" degrade selectivity.\n");
printf(" -ps Lower scoring thresholds to 95%% of default levels.\n");
printf(" -ps Change scoring thresholds to percent of default levels.\n");
printf(" -rp Flag possible pseudogenes (score < 100 or tRNA anticodon\n");
printf(" loop <> 7 bases long). Note that genes with score < 100\n");
printf(" will not be detected or flagged if scoring thresholds are not\n");
printf(" also changed to below 100%% (see -ps switch).\n");
printf(" -seq Print out primary sequence.\n");
printf(" -br Show secondary structure of tRNA gene primary\n");
printf(" sequence with round brackets.\n");
printf(" -fasta Print out primary sequence in fasta format.\n");
printf(" -fo Print out primary sequence in fasta format only\n");
printf(" (no secondary structure).\n");
printf(" -fon Same as -fo, with sequence and gene numbering in header.\n");
printf(" -fos Same as -fo, with no spaces in header.\n");
printf(" -fons Same as -fo, with sequence and gene numbering, but no spaces.\n");
printf(" -j Display 4-base sequence on 3' end of astem\n");
printf(" regardless of predicted amino-acyl acceptor\n");
printf(" length.\n");
printf(" -jr Allow some divergence of 3' ");
printf("amino-acyl acceptor\n");
printf(" sequence from NCCA.\n");
printf(" -jr4 Allow some divergence of 3' ");
printf("amino-acyl acceptor\n");
printf(" sequence from NCCA, and display 4 bases.\n");
printf(" -v Verbose. Prints out search progress\n");
printf(" to STDERR.\n");
printf(" -a Print out tRNA domain for tmRNA genes\n");
printf(" -o print output into . If \n");
printf(" exists, it is overwritten.\n");
printf(" By default, output goes to STDOUT.\n");
printf(" -w Print out genes in batch mode.\n");
printf(" For tRNA genes, output is in the form:\n\n");
printf(" Sequence name\n");
printf(" N genes found\n");
printf(" 1 tRNA- [locus 1]");
printf(" (nnn)\n");
printf(" i(,)\n");
printf(" . \n");
printf(" . \n");
printf(" N tRNA- [Locus N]");
printf(" (nnn)\n");
printf(" i(,)\n");
printf("\n N is the number of genes found\n");
printf(" is the tRNA iso-acceptor species\n");
printf(" is the tRNA anticodon ");
printf("relative position\n");
printf(" (nnn) is the tRNA anticodon base triplet\n");
printf(" i means the tRNA gene has a C-loop intron\n");
printf("\n For tmRNA genes, output is in the form:\n");
printf("\n n tmRNA(p) [Locus n] ,");
printf("\n");
printf(" \n\n");
printf(" p means the tmRNA gene is permuted\n");
printf("\n\n"); }
void error_report(int n, char *s)
{ switch(n)
{ case 0: fprintf(stderr,
"-%s not recognised, type aragorn -h for help\n",s);
break;
case 1: fprintf(stderr,
"-%s not understood, type aragorn -h for help\n",s);
break;
case 2: fprintf(stderr,"Could not open %s\n",s);
break;
case 3: fprintf(stderr,
"No sequence file specified, type aragorn -h for help\n");
break;
case 4: fprintf(stderr,"Don't know genetic code %s\n",s);
break;
case 5: fprintf(stderr,"Too many genetic code modifications (max=%d)\n",
MAXGCMOD);
break;
default: break; }
exit(0); }
void process_genecode_switch(char *s, csw *sw)
{ int i,m,lmax,len[NGENECODE],anticodon,b[3];
long l;
char c,*ss,*se;
static char genecodetag[NGENECODE][10] =
{ "MET",
"STD","VERT","YEAST","PROT","INVERT",
"CILIATE","DELETED","DELETED","FLATWORM","EUPLOT",
"BACT","ALTYEAST","ASCID","ALTFLAT","BLEP",
"CHLOROPH","DELETED","DELETED","DELETED","DELETED",
"TREM","SCEN","THRAUST" };
sw->geneticcode = STANDARD;
sw->gcfix = 1;
c = *s;
if (c >= '0')
if (c <= '9')
{ lconvert(s,&l);
i = (int)l;
if ((i >= 0) && (i < NGENECODE)) sw->geneticcode = i;
goto MOD; }
for (i = 0; i < NGENECODE; i++)
{ len[i] = 0;
ss = s;
se = genecodetag[i];
while (c == *ss++)
{ if (upcasec(c) != *se++) break;
len[i]++; }}
m = -1;
lmax = 0;
i = -1;
while (++i < NGENECODE)
if (len[i] > lmax)
{ m = i;
lmax = len[i]; }
if (m >= 0) sw->geneticcode = m;
else error_report(4,s);
MOD:
sw->ngcmod = 0;
ss = s;
while (ss = strpos(ss,","))
{ if (sw->ngcmod >= MAXGCMOD) error_report(5,NULL);
ss++;
for (i = 0; i < 3; i++)
{ b[i] = Adenine;
c = upcasec(ss[i]);
if (c == 'C') b[i] = Cytosine;
if (c == 'G') b[i] = Guanine;
if (c == 'T') b[i] = Thymine;
if (c == 'U') b[i] = Thymine; }
anticodon = ((Thymine - b[2])<<4) + ((Thymine - b[1])<<2) + (Thymine - b[0]);
if (!(se = strpos(ss,"="))) break;
se++;
for (i = 0; i < NAMINOACID; i++)
if (upcasec(se[0]) == upcasec(aaname[i][0]))
if (upcasec(se[1]) == upcasec(aaname[i][1]))
if (upcasec(se[2]) == upcasec(aaname[i][2]))
{ aamap[sw->geneticcode][anticodon] = i;
sw->gcmod[sw->ngcmod] = anticodon;
sw->ngcmod++;
break; } }}
void change_thresholds(csw *sw, double psthresh)
{
sw->cdsthresh *= psthresh;
sw->srpthresh *= psthresh;
sw->tmrnathresh *= psthresh;
sw->mtdtthresh *= psthresh;
sw->mttthresh *= psthresh;
sw->mtdthresh *= psthresh;
sw->trnathresh *= psthresh;
}
int main(int z, char *v[])
{ int i,lv,filecounter;
long l;
double psthresh;
char c1,c2,c3,c4,*s;
data_set d;
static csw sw =
{ NULL,0,0,0,0,0,0,0,1,0,0,
STANDARD,0,{0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0},0,METAZOAN_MT,
1,0,5,5,1,0,0,0,2,0,0,0,0,0,0,3,0,2,1,1,0,0,0,0,0,0,0,0,1,
0,0,0,0,0,0,0,{0,0,0,0,0},0,0,{0,0,0,0,0},0,0,0,0,0,0,0,0,0L,
tRNAthresh,4.0,29.0,26.0,7.5,8.0,
mtRNAtthresh,mtRNAdthresh,mtRNAdtthresh,-7.9,-6.0,
tmRNAthresh,14.0,10.0,25.0,9.0,srpRNAthresh,CDSthresh,
{tRNAthresh,tmRNAthresh,srpRNAthresh,0.0,CDSthresh },
{ 45, 45, 45, 45, 45, 45, 45, 45, 45, 45,
45, 45, 45, 45, 45, 45, 45, 45, 45, 45,
45, 45, 45, 45, 45, 45, 45, 45, 45, 45,
10, 65, 82, 65, 71, 79, 82, 78, 32,
118, 49, 46, 50, 46, 51, 54, 32, 32, 32,
68, 101, 97,110, 32, 76, 97, 115, 108,
101, 116, 116, 10,
45, 45, 45, 45, 45, 45, 45, 45, 45, 45,
45, 45, 45, 45, 45, 45, 45, 45, 45, 45,
45, 45, 45, 45, 45, 45, 45, 45, 45, 45,
10, TERM }};
sw.f = stdout;
filecounter = 0;
i = 0;
while (++i < z)
if (*(v[i]) == '-')
{ lv = length(v[i]);
if (lv < 2) continue;
s = v[i] + 1;
c1 = upcasec(*s);
c2 = (lv > 2)?upcasec(s[1]):' ';
c3 = (lv > 3)?upcasec(s[2]):' ';
c4 = (lv > 4)?upcasec(s[3]):' ';
switch(c1)
{ case 'E': sw.energydisp = (c2 == 'S')?2:1;
break;
case 'A': if (c2 == '7') sw.extastem = 0;
else
if (c2 == 'A') sw.matchacceptor = 1;
else sw.secstructdisp = 1;
break;
case 'B': if (c2 == 'R') sw.seqdisp = 2;
else sw.libflag = 1;
break;
case 'X': sw.libflag = 2;
break;
case 'W': if (sw.batch < 1) sw.batch = 1;
break;
case 'V': sw.verbose = 1;
break;
case 'S': if (c2 == 'S')
{ sw.sp1max = 2;
sw.sp2min = 1;
sw.sp2max = 1;
break; }
if (c2 == 'E')
{ if (sw.seqdisp < 1) sw.seqdisp = 1;
break; }
if ((c2 == 'C') || (c2 == '-'))
{ sw.both = 1;
break; }
sw.both = 0;
break;
case 'F': if (softstrpos(s,"O"))
{ sw.batch = 2;
if (softstrpos(s,"S")) sw.batch |= 0x4;
if (softstrpos(s,"N")) sw.batch |= 0x8;
if (softstrpos(s,"C")) sw.batch |= 0x10; }
else
{ if (softstrpos(s,"C")) sw.seqdisp = 4;
else sw.seqdisp = 3; }
break;
case 'D': sw.both = 2;
break;
case 'L': sw.linear = 1;
break;
case 'C': if (c2 == '7') sw.cloop7 = 1;
else sw.linear = 0;
break;
case 'J': if (lv > 2)
{ if (c2 == 'R') sw.aataildiv = 1;
if (c3 == '4') sw.aataildisp = 1; }
else sw.aataildisp = 1;
break;
case '1': sw.minintronlen = 10;
break;
case 'I': if (c2 == 'O') { sw.ioverlay = 1; s++; lv--; }
else if (c2 == 'F') { sw.ifixedpos = 1; s++; lv--; }
else if (c2 == 'R') { sw.ireportminintronlen = 1; s++; lv--; }
if (c3 == 'O') { sw.ioverlay = 1; s++; lv--; }
else if (c3 == 'F') { sw.ifixedpos = 1; s++; lv--; }
else if (c3 == 'R') { sw.ireportminintronlen = 1; s++; lv--; }
if (c4 == 'O') { sw.ioverlay = 1; s++; lv--; }
else if (c4 == 'F') { sw.ifixedpos = 1; s++; lv--; }
else if (c4 == 'R') { sw.ireportminintronlen = 1; s++; lv--; }
if (lv > 2) s = lconvert(s+1,&l);
else goto IMAX;
if (*s == ',')
{ if (sw.ireportminintronlen == 1)
sw.minintronlenreport = (int)l;
else
sw.minintronlen = (int)l;
lconvert(s+1,&l);
sw.maxintronlen = (int)l; }
else sw.maxintronlen = (int)l;
if (sw.maxintronlen > (LSEQ - MAXTRNALEN))
sw.maxintronlen = (LSEQ - MAXTRNALEN);
if (sw.maxintronlen > MAXINTRONLEN)
sw.maxintronlen = MAXINTRONLEN;
if ((sw.minintronlen < 0) ||
(sw.maxintronlen < sw.minintronlen))
error_report(1,v[i]);
if ((sw.minintronlenreport < 0) ||
(sw.maxintronlen < sw.minintronlenreport))
error_report(1,v[i]);
break;
IMAX:
sw.maxintronlen = MAXINTRONLEN;
break;
case 'T': if (c2 == 'V')
{ sw.tvloop = 0;
break; }
sw.trna = 1;
if (lv > 2)
{ s = dconvert(s+1,&sw.trnathresh);
if (*s == ',') dconvert(s+1,&sw.ttarmthresh); }
break;
case 'M': if (c2 == 'T')
{ sw.mtrna = 1;
if (!sw.gcfix) sw.geneticcode = METAZOAN_MT;
if (lv > 3)
{ s += 2;
c3 = upcasec(*s);
if (c3 == 'M')
{ do c3 = upcasec(*++s);
while ((c3 == 'A') || (c3 == 'M')
|| (c3 == 'L'));
sw.tvloop = 0;
sw.geneticcode = VERTEBRATE_MT;
sw.discrim = MAMMAL_MT; }
MTNXTC:
if (c3 == 'X')
{ c3 = upcasec(*++s);
sw.mtxdetect = 0;
goto MTNXTC; }
if (c3 == 'C')
{ c3 = upcasec(*++s);
sw.mtcdsscan = 0;
goto MTNXTC; }
if (c3 == 'D')
{ c3 = upcasec(*++s);
sw.mtcompov = 1;
goto MTNXTC; }
if (c3 != '-')
if (c3 != '.')
if ((c3 < '0') || (c3 > '9'))
break;
s = dconvert(s,&sw.mtdtthresh);
if (*s == ',') s = dconvert(s+1,&sw.mttthresh);
if (*s == ',') s = dconvert(s+1,&sw.mtdthresh);
if (*s == ',') s = dconvert(s+1,&sw.mttarmthresh);
if (*s == ',') dconvert(s+1,&sw.mtdarmthresh); }}
else
{ sw.tmrna = 1;
if (lv > 2)
dconvert(s+1,&sw.tmrnathresh); }
break;
case 'P': if (c2 == 'S')
{ if (c3 != '-')
if (c3 != '.')
if ((c3 < '0') || (c3 > '9'))
{ change_thresholds(&sw,PSEUDOGENElevel);
break; }
psthresh = 1.0;
dconvert(s+2,&psthresh);
change_thresholds(&sw,psthresh);
break; }
break;
case 'G': if (c2 != 'C') break;
process_genecode_switch(s+2,&sw);
break;
case 'R': if (c2 == 'N') sw.repeatsn = 1;
else
if (c2 == 'P') sw.reportpseudogenes = 1;
else sw.tmstrict = 0;
break;
case 'Q': sw.showconfig = 0;
break;
case 'H': aragorn_help_menu();
exit(0);
case 'O': if (lv > 2)
s++;
else
{ if (++i >= z) break;
s = v[i]; }
sw.f = fopen(s,"w");
if (!sw.f) error_report(2,s);
break;
default: error_report(0,s); }}
else
if (filecounter < 1)
{ d.f = fopen(v[i],"r");
if (d.f)
filecounter++;
else
error_report(2,v[i]); }
else
if (filecounter < 2)
{ sw.f = fopen(v[i],"w");
if (!sw.f) error_report(2,v[i]);
filecounter++; }
else
error_report(0,v[i]);
if (filecounter < 1)
error_report(3,NULL);
if ((!sw.trna) & (!sw.tmrna))
{ sw.trna = 1;
sw.tmrna = 1; }
if (sw.mtrna) sw.trna = 0;
ts = (gene *)malloc(NT*sizeof(gene));
if (ts == NULL)
{ fprintf(stderr,"Not enough memory available to store detected genes\n");
exit(1); }
sw.genespace = NT;
if (sw.libflag) fprintf(sw.f,"Library\n");
if (sw.batch) bopt_fastafile(&d,&sw);
else iopt_fastafile(&d,&sw);
free((void *)ts);
fclose(d.f);
if (!sw.batch && sw.showconfig)
{ fprintf(sw.f,"Configuration: ");
i = -1;
while (++i < z) fprintf(sw.f,"%s ",v[i]);
fputc('\n',sw.f); }
if (sw.f != stdout) fclose(sw.f);
return(0); }