[med-svn] r13067 - in trunk/packages/aragorn/trunk/debian: . man
Sascha Steinbiss
sascha-guest at alioth.debian.org
Sat Feb 23 11:31:12 UTC 2013
Author: sascha-guest
Date: 2013-02-23 11:31:12 +0000 (Sat, 23 Feb 2013)
New Revision: 13067
Modified:
trunk/packages/aragorn/trunk/debian/man/aragorn.1
trunk/packages/aragorn/trunk/debian/manpage.1.src
Log:
improve man page
Modified: trunk/packages/aragorn/trunk/debian/man/aragorn.1
===================================================================
--- trunk/packages/aragorn/trunk/debian/man/aragorn.1 2013-02-23 09:50:39 UTC (rev 13066)
+++ trunk/packages/aragorn/trunk/debian/man/aragorn.1 2013-02-23 11:31:12 UTC (rev 13067)
@@ -31,137 +31,351 @@
aragorn \- detect tRNA genes in nucleotide sequences
.SH "SYNOPSIS"
.sp
-\fBaragorn\fR \-v \-s \-d \-c \-l \-j \-a \-q \-rn \-w \-ifro<min>,<max> \-t \-m \-mt \-gc \-tv \-seq \-br \-fasta \-fo \-o <outfile> <filename>
+\fBaragorn\fR [\fIOPTION\fR]\&... \fIFILE\fR
.SH "OPTIONS"
-.sp
-.if n \{\
+.PP
+\fB\-m\fR
.RS 4
-.\}
-.nf
-\-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\&.
-\-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=<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\&.
-\-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\&.\en");
-\-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\*(Aq end of astem
- regardless of predicted amino\-acyl acceptor length\&.
-\-jr Allow some divergence of 3\*(Aq amino\-acyl acceptor
- sequence from NCCA\&.
-\-jr4 Allow some divergence of 3\*(Aq 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\&.
-.fi
-.if n \{\
+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\&. \-i,\-sr 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 \-gcvert,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
-<filename> 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\&.
+[\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 at acgt\&.se>, Dean Laslett <gaiaquark at gmail\&.com>
Modified: trunk/packages/aragorn/trunk/debian/manpage.1.src
===================================================================
--- trunk/packages/aragorn/trunk/debian/manpage.1.src 2013-02-23 09:50:39 UTC (rev 13066)
+++ trunk/packages/aragorn/trunk/debian/manpage.1.src 2013-02-23 11:31:12 UTC (rev 13067)
@@ -10,129 +10,230 @@
SYNOPSIS
--------
-*aragorn* -v -s -d -c -l -j -a -q -rn -w -ifro<min>,<max> -t -m -mt
- -gc -tv -seq -br -fasta -fo -o <outfile> <filename>
+*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.
- -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=<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.
- -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.\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 <outfile> Print output to <outfile>. If <outfile>
- already exists, it is overwritten. By default
- all output goes to stdout.
+*-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
-----------
@@ -140,7 +241,7 @@
A minimum requirement is at least a 32 bit compiler architecture
(variable types int and unsigned int are at least 4 bytes long).
-<filename> is assumed to contain one or more sequences
+['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
More information about the debian-med-commit
mailing list