390 lines
8.9 KiB
Groff
390 lines
8.9 KiB
Groff
'\" t
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.\" Title: aragorn
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.\" Author: [see the "AUTHORS" section]
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.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
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.\" Date: 02/24/2013
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.\" Manual: \ \&
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.\" Source: \ \&
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.\" Language: English
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.\"
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.TH "ARAGORN" "1" "02/24/2013" "\ \&" "\ \&"
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.\" -----------------------------------------------------------------
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.\" * Define some portability stuff
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.\" -----------------------------------------------------------------
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.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.\" http://bugs.debian.org/507673
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.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
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.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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.ie \n(.g .ds Aq \(aq
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.el .ds Aq '
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.\" -----------------------------------------------------------------
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.\" * set default formatting
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.\" -----------------------------------------------------------------
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.\" disable hyphenation
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.nh
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.\" disable justification (adjust text to left margin only)
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.ad l
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.\" -----------------------------------------------------------------
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.\" * MAIN CONTENT STARTS HERE *
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.\" -----------------------------------------------------------------
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.SH "NAME"
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aragorn \- detect tRNA genes in nucleotide sequences
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.SH "SYNOPSIS"
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.sp
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\fBaragorn\fR [\fIOPTION\fR]\&... \fIFILE\fR
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.SH "OPTIONS"
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.PP
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\fB\-m\fR
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.RS 4
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Search for tmRNA genes\&.
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.RE
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.PP
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\fB\-t\fR
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.RS 4
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Search for tRNA genes\&. By default, all are detected\&. If one of
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\fB\-m\fR
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or
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\fB\-t\fR
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is specified, then the other is not detected unless specified as well\&.
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.RE
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.PP
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\fB\-mt\fR
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.RS 4
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Search for Metazoan mitochondrial tRNA genes\&. tRNA genes with introns not detected\&.
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\fB\-i\fR,
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\fB\-sr\fR
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switchs ignored\&. Composite Metazoan mitochondrial genetic code used\&.
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.RE
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.PP
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\fB\-mtmam\fR
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.RS 4
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Search for Mammalian mitochondrial tRNA genes\&.
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\fB\-i\fR,
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\fB\-sr\fR
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switchs ignored\&.
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\fB\-tv\fR
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switch set\&. Mammalian mitochondrial genetic code used\&.
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.RE
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.PP
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\fB\-mtx\fR
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.RS 4
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Same as
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\fB\-mt\fR
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but low scoring tRNA genes are not reported\&.
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.RE
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.PP
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\fB\-mtd\fR
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.RS 4
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Overlapping metazoan mitochondrial tRNA genes on opposite strands are reported\&.
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.RE
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.PP
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\fB\-gc\fR[\fInum\fR]
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.RS 4
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Use the GenBank transl_table = [\fInum\fR] genetic code\&. Individual modifications can be appended using
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\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
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\fB\-gcvert\fR,aga=Trp,agg=Trp uses the Vertebrate Mitochondrial code and the codons AGA and AGG changed to Tryptophan\&.
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.RE
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.PP
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\fB\-gcstd\fR
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.RS 4
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Use standard genetic code\&.
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.RE
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.PP
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\fB\-gcmet\fR
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.RS 4
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Use composite Metazoan mitochondrial genetic code\&.
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.RE
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.PP
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\fB\-gcvert\fR
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.RS 4
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Use Vertebrate mitochondrial genetic code\&.
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.RE
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.PP
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\fB\-gcinvert\fR
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.RS 4
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Use Invertebrate mitochondrial genetic code\&.
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.RE
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.PP
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\fB\-gcyeast\fR
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.RS 4
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Use Yeast mitochondrial genetic code\&.
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.RE
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.PP
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\fB\-gcprot\fR
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.RS 4
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Use Mold/Protozoan/Coelenterate mitochondrial genetic code\&.
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.RE
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.PP
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\fB\-gcciliate\fR
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.RS 4
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Use Ciliate genetic code\&.
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.RE
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.PP
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\fB\-gcflatworm\fR
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.RS 4
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Use Echinoderm/Flatworm mitochondrial genetic code
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.RE
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.PP
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\fB\-gceuplot\fR
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.RS 4
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Use Euplotid genetic code\&.
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.RE
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.PP
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\fB\-gcbact\fR
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.RS 4
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Use Bacterial/Plant Chloroplast genetic code\&.
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.RE
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.PP
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\fB\-gcaltyeast\fR
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.RS 4
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Use alternative Yeast genetic code\&.
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.RE
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.PP
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\fB\-gcascid\fR
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.RS 4
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Use Ascidian Mitochondrial genetic code\&.
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.RE
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.PP
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\fB\-gcaltflat\fR
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.RS 4
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Use alternative Flatworm Mitochondrial genetic code\&.
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.RE
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.PP
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\fB\-gcblep\fR
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.RS 4
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Use Blepharisma genetic code\&.
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.RE
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.PP
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\fB\-gcchloroph\fR
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.RS 4
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Use Chlorophycean Mitochondrial genetic code\&.
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.RE
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.PP
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\fB\-gctrem\fR
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.RS 4
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Use Trematode Mitochondrial genetic code\&.
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.RE
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.PP
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\fB\-gcscen\fR
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.RS 4
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Use Scenedesmus obliquus Mitochondrial genetic code\&.
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.RE
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.PP
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\fB\-gcthraust\fR
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.RS 4
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Use Thraustochytrium Mitochondrial genetic code\&.
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.RE
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.PP
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\fB\-tv\fR
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.RS 4
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Do not search for mitochondrial TV replacement loop tRNA genes\&. Only relevant if
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\fB\-mt\fR
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used\&.
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.RE
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.PP
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\fB\-c7\fR
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.RS 4
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Search for tRNA genes with 7 base C\-loops only\&.
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.RE
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.PP
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\fB\-i\fR
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.RS 4
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Search for tRNA genes with introns in anticodon loop with maximum length 3000 bases\&. Minimum intron length is 0 bases\&. Ignored if
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\fB\-m\fR
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is specified\&.
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.RE
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.PP
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\fB\-i\fR[\fImax\fR]
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.RS 4
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Search for tRNA genes with introns in anticodon loop with maximum length [\fImax\fR] bases\&. Minimum intron length is 0 bases\&. Ignored if
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\fB\-m\fR
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is specified\&.
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.RE
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.PP
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\fB\-i\fR[\fImin\fR],[\fImax\fR]
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.RS 4
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Search for tRNA genes with introns in anticodon loop with maximum length [\fImax\fR] bases, and minimum length [\fImin\fR] bases\&. Ignored if
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\fB\-m\fR
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is specified\&.
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.RE
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.PP
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\fB\-io\fR
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.RS 4
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Same as
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\fB\-i\fR, but allow tRNA genes with long introns to overlap shorter tRNA genes\&.
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.RE
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.PP
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\fB\-if\fR
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.RS 4
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Same as
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\fB\-i\fR, but fix intron between positions 37 and 38 on C\-loop (one base after anticodon)\&.
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.RE
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.PP
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\fB\-ifo\fR
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.RS 4
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Same as
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\fB\-if\fR
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and
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\fB\-io\fR
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combined\&.
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.RE
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.PP
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\fB\-ir\fR
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.RS 4
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Same as
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\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\&.
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.RE
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.PP
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\fB\-c\fR
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.RS 4
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Assume that each sequence has a circular topology\&. Search wraps around each end\&. Default setting\&.
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.RE
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.PP
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\fB\-l\fR
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.RS 4
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Assume that each sequence has a linear topology\&. Search does not wrap\&.
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.RE
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.PP
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\fB\-d\fR
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.RS 4
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Double\&. Search both strands of each sequence\&. Default setting\&.
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.RE
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.PP
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\fB\-s\fR or \fB\-s+\fR
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.RS 4
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Single\&. Do not search the complementary (antisense) strand of each sequence\&.
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.RE
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.PP
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\fB\-sc\fR or \fB\-s\-\fR
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.RS 4
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Single complementary\&. Do not search the sense strand of each sequence\&.
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.RE
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.PP
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\fB\-ps\fR
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.RS 4
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Lower scoring thresholds to 95% of default levels\&.
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.RE
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.PP
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\fB\-ps\fR[\fInum\fR]
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.RS 4
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Change scoring thresholds to [\fInum\fR] percent of default levels\&.
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.RE
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.PP
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\fB\-rp\fR
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.RS 4
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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)\&.
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.RE
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.PP
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\fB\-seq\fR
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.RS 4
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Print out primary sequence\&.
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.RE
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.PP
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\fB\-br\fR
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.RS 4
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Show secondary structure of tRNA gene primary sequence using round brackets\&.
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.RE
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.PP
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\fB\-fasta\fR
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.RS 4
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Print out primary sequence in fasta format\&.
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.RE
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.PP
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\fB\-fo\fR
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.RS 4
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Print out primary sequence in fasta format only (no secondary structure)\&.
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.RE
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.PP
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\fB\-fon\fR
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.RS 4
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Same as
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\fB\-fo\fR, with sequence and gene numbering in header\&.
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.RE
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.PP
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\fB\-fos\fR
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.RS 4
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Same as
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\fB\-fo\fR, with no spaces in header\&.
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.RE
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.PP
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\fB\-fons\fR
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.RS 4
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Same as
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\fB\-fo\fR, with sequence and gene numbering, but no spaces\&.
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.RE
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.PP
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\fB\-w\fR
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.RS 4
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Print out in Batch mode\&.
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.RE
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.PP
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\fB\-ss\fR
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.RS 4
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Use the stricter canonical 1\-2 bp spacer1 and 1 bp spacer2\&. Ignored if
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\fB\-mt\fR
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set\&. Default is to allow 3 bp spacer1 and 0\-2 bp spacer2, which may degrade selectivity\&.
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.RE
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.PP
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\fB\-v\fR
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.RS 4
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Verbose\&. Prints out information during search to STDERR\&.
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.RE
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.PP
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\fB\-a\fR
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.RS 4
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Print out tRNA domain for tmRNA genes\&.
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.RE
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.PP
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\fB\-a7\fR
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.RS 4
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Restrict tRNA astem length to a maximum of 7 bases
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.RE
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.PP
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\fB\-aa\fR
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.RS 4
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Display message if predicted iso\-acceptor species does not match species in sequence name (if present)\&.
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.RE
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.PP
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\fB\-j\fR
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.RS 4
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Display 4\-base sequence on 3\*(Aq end of astem regardless of predicted amino\-acyl acceptor length\&.
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.RE
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.PP
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\fB\-jr\fR
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.RS 4
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Allow some divergence of 3\*(Aq amino\-acyl acceptor sequence from NCCA\&.
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.RE
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.PP
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\fB\-jr4\fR
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.RS 4
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Allow some divergence of 3\*(Aq amino\-acyl acceptor sequence from NCCA, and display 4 bases\&.
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.RE
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.PP
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\fB\-q\fR
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.RS 4
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Dont print configuration line (which switchs and files were used)\&.
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.RE
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.PP
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\fB\-rn\fR
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.RS 4
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Repeat sequence name before summary information\&.
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.RE
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.PP
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\fB\-O\fR [\fIoutfile\fR]
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.RS 4
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Print output to
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\fI\&. If [\*(Aqoutfile\fR] already exists, it is overwritten\&. By default all output goes to stdout\&.
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.RE
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.SH "DESCRIPTION"
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.sp
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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)\&.
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.sp
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[\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\&.
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.SH "AUTHORS"
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.sp
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Bjorn Canback <bcanback@acgt\&.se>, Dean Laslett <gaiaquark@gmail\&.com>
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.SH "REFERENCES"
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.sp
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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
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.sp
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Laslett, D\&. and Canback, B\&. (2008) ARWEN: a program to detect tRNA genes in metazoan mitochondrial nucleotide sequences Bioinformatics, 24(2); 172\-175\&. |