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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.
-
-
-
-
-
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