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'\" 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
switches 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
switches 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
Do not print configuration line (which switches 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\&.