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commit 9392bc1d84ed62d50143d922b898fc1712bf0097 Author: Sascha Steinbiss <sa...@debian.org> Date: Wed Oct 12 07:14:21 2016 +0000 New upstream version 1.2.38 --- aragorn.1 | 390 +++++++++++++++++++++++++++++++++++++ aragorn1.2.37.c => aragorn1.2.38.c | 25 ++- manpage.1.src | 273 -------------------------- 3 files changed, 405 insertions(+), 283 deletions(-) diff --git a/aragorn.1 b/aragorn.1 new file mode 100644 index 0000000..617405f --- /dev/null +++ b/aragorn.1 @@ -0,0 +1,390 @@ +'\" t +.\" Title: aragorn +.\" Author: [see the "AUTHORS" section] +.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/> +.\" 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=<aa> B = A,C,G, or T\&. <aa> 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 <bcanback@acgt\&.se>, Dean Laslett <gaiaquark@gmail\&.com> +.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\&. diff --git a/aragorn1.2.37.c b/aragorn1.2.38.c similarity index 97% rename from aragorn1.2.37.c rename to aragorn1.2.38.c index 8db114b..1b05cbe 100644 --- a/aragorn1.2.37.c +++ b/aragorn1.2.38.c @@ -1,7 +1,7 @@ /* --------------------------------------------------------------- -ARAGORN v1.2.37 Dean Laslett +ARAGORN v1.2.38 Dean Laslett --------------------------------------------------------------- ARAGORN (together with ARWEN at last) @@ -15,7 +15,7 @@ ARAGORN v1.2.37 Dean Laslett E-mail: Dean Laslett: gaiaqu...@gmail.com Bj�rn Canb�ck: bcanb...@acgt.se - Version 1.2.37 Oct 15th, 2014. + Version 1.2.38 Oct 8th, 2016. Thanks to Francisco Ossandon for finding many bugs and testing Thanks to Haruo Suzuki for finding bugs Thanks to Sascha Steinbiss for fixing bugs @@ -327,7 +327,7 @@ DAMAGES. --------------------------------------------------------------- -ARAGORN v1.2.37 Dean Laslett +ARAGORN v1.2.38 Dean Laslett --------------------------------------------------------------- */ @@ -772,7 +772,8 @@ typedef struct { char genetypename[NS][10]; int lacds; int ldcds; long nabase; - double pseudogenethresh; + double reportpsthresh; + double threshlevel; double trnathresh; double ttscanthresh; double ttarmthresh; @@ -1596,7 +1597,7 @@ ftp://ftp.ncbi.nih.gov/entrez/misc/data/gc.prt char helpmenu[NHELPLINE][81] = { "----------------------------", -"ARAGORN v1.2.37 Dean Laslett", +"ARAGORN v1.2.38 Dean Laslett", "----------------------------\n", "Please reference the following papers if you use this", "program as part of any published research.\n", @@ -5134,7 +5135,7 @@ void disp_cds(FILE *f, gene *t, csw *sw) int pseudogene(gene *t, csw *sw) { -if (t->energy < sw->pseudogenethresh) return(1); +if (t->energy < sw->reportpsthresh) return(1); if (t->genetype == tRNA) if (t->cloop != 7) return(1); @@ -5655,7 +5656,7 @@ int find_tstems(int *s, int ls, trna_loop hit[], int nh, csw *sw) static int tem_tmrna[6] = { 0x0100, 0x0002, 0x2220, 0x0220, 0x0000, 0x0000 }; i = 0; - tem = (sw->tmrna)?tem_tmrna:tem_trna; + tem = (sw->tmrna || (sw->threshlevel < 1.0))?tem_tmrna:tem_trna; ithresh1 = (int)sw->ttscanthresh; thresh2 = sw->ttarmthresh; ss = s + sw->loffset; @@ -9707,6 +9708,9 @@ int tmioptimise(data_set *d, int *seq, int lseq, int nts, csw *sw) nts = tmopt_perm(d,thit+nt,tarm,the,ahit+nah,nppah,nts,seq,sw); if (thet < tarmthresh) continue; the = thet; } + else if (sw->threshlevel < 1.0) /* find_tstems is generating extra tstems */ + { the -= (G[tpos[t.tstem]] + G[tpos[t.tstem+1]]); + if (the < tarmthresh) continue; } if (!sw->trna) continue; na = -1; while (++na < nah) @@ -11453,6 +11457,7 @@ void process_genecode_switch(char *s, csw *sw) void change_thresholds(csw *sw, double psthresh) { +sw->threshlevel = psthresh; sw->cdsthresh *= psthresh; sw->srpthresh *= psthresh; sw->tmrnathresh *= psthresh; @@ -11476,7 +11481,7 @@ int main(int z, char *v[]) 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,NTAG,10,30, {0,0,0,0,0,0},{0,0,0,0,0,0},{0,0,0,0,0,0},0,0,0,0,0L, - 100.0,tRNAthresh,4.0,29.0,26.0,7.5,8.0, + 100.0,1.0,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 }, @@ -11484,7 +11489,7 @@ int main(int z, char *v[]) 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, 55, 32, 32, 32, + 118, 49, 46, 50, 46, 51, 56, 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, @@ -11690,7 +11695,7 @@ int main(int z, char *v[]) if (c2 == 'P') { sw.reportpseudogenes = 1; if (lv > 3) - dconvert(s+2,&sw.pseudogenethresh); } + dconvert(s+2,&sw.reportpsthresh); } else sw.tmstrict = 0; break; case 'Q': sw.showconfig = 0; diff --git a/manpage.1.src b/manpage.1.src deleted file mode 100644 index 26b9c6d..0000000 --- a/manpage.1.src +++ /dev/null @@ -1,273 +0,0 @@ -ARAGORN(1) -========== - -NAME ----- - -aragorn - detect tRNA genes in nucleotide sequences - - -SYNOPSIS --------- - -*aragorn* ['OPTION']... 'FILE' - - -OPTIONS -------- - -*-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*['num']:: - Use the GenBank transl_table = ['num'] genetic code. - Individual modifications can be appended using - ',BBB'=<aa> B = A,C,G, or T. <aa> 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. - -*-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. - -*-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*['max']:: - Search for tRNA genes with introns in - anticodon loop with maximum length ['max'] - bases. Minimum intron length is 0 bases. - Ignored if *-m* is specified. - -*-i*['min'],['max']:: - Search for tRNA genes with introns in - anticodon loop with maximum length ['max'] - bases, and minimum length ['min'] 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 ['min'] bases rather than search for - tRNA genes with minimum length ['min'] bases. - With this switch, ['min'] 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*['num']:: - Change scoring thresholds to ['num'] 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. - -*-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* ['outfile']:: - Print output to ['outfile]'. If ['outfile'] - already exists, it is overwritten. By default - all output goes to stdout. - -DESCRIPTION ------------ - -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). - -['FILE'] 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. - - -AUTHORS ------- - -Bjorn Canback <bcanb...@acgt.se>, Dean Laslett <gaiaqu...@gmail.com> - - -REFERENCES ----------- - -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. - - - - - -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/aragorn.git _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit