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'\" t
.\" Title: GETORF
.\" Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
.\" Date: 05/11/2012
.\" Manual: EMBOSS Manual for Debian
.\" Source: EMBOSS 6.4.0
.\" Language: English
.\"
.TH "GETORF" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
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.nh
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.SH "NAME"
getorf \- Finds and extracts open reading frames (ORFs)
.SH "SYNOPSIS"
.HP \w'\fBgetorf\fR\ 'u
\fBgetorf\fR \fB\-sequence\ \fR\fB\fIseqall\fR\fR [\fB\-table\ \fR\fB\fIlist\fR\fR] [\fB\-minsize\ \fR\fB\fIinteger\fR\fR] [\fB\-maxsize\ \fR\fB\fIinteger\fR\fR] [\fB\-find\ \fR\fB\fIlist\fR\fR] \fB\-methionine\ \fR\fB\fIboolean\fR\fR \fB\-circular\ \fR\fB\fIboolean\fR\fR \fB\-reverse\ \fR\fB\fIboolean\fR\fR \fB\-flanking\ \fR\fB\fIinteger\fR\fR \fB\-outseq\ \fR\fB\fIseqoutall\fR\fR
.HP \w'\fBgetorf\fR\ 'u
\fBgetorf\fR \fB\-help\fR
.SH "DESCRIPTION"
.PP
\fBgetorf\fR
is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Gene finding" command group(s)\&.
.SH "OPTIONS"
.SS "Input section"
.PP
\fB\-sequence\fR \fIseqall\fR
.RS 4
.RE
.SS "Additional section"
.PP
\fB\-table\fR \fIlist\fR
.RS 4
.RE
.PP
\fB\-minsize\fR \fIinteger\fR
.RS 4
Default value: 30
.RE
.PP
\fB\-maxsize\fR \fIinteger\fR
.RS 4
Default value: 1000000
.RE
.PP
\fB\-find\fR \fIlist\fR
.RS 4
This is a small menu of possible output options\&. The first four options are to select either the protein translation or the original nucleic acid sequence of the open reading frame\&. There are two possible definitions of an open reading frame: it can either be a region that is free of STOP codons or a region that begins with a START codon and ends with a STOP codon\&. The last three options are probably only of interest to people who wish to investigate the statistical properties of the regions around potential START or STOP codons\&. The last option assumes that ORF lengths are calculated between two STOP codons\&.
.RE
.SS "Advanced section"
.PP
\fB\-methionine\fR \fIboolean\fR
.RS 4
START codons at the beginning of protein products will usually code for Methionine, despite what the codon will code for when it is internal to a protein\&. This qualifier sets all such START codons to code for Methionine by default\&. Default value: Y
.RE
.PP
\fB\-circular\fR \fIboolean\fR
.RS 4
Default value: N
.RE
.PP
\fB\-reverse\fR \fIboolean\fR
.RS 4
Set this to be false if you do not wish to find ORFs in the reverse complement of the sequence\&. Default value: Y
.RE
.PP
\fB\-flanking\fR \fIinteger\fR
.RS 4
If you have chosen one of the options of the type of sequence to find that gives the flanking sequence around a STOP or START codon, this allows you to set the number of nucleotides either side of that codon to output\&. If the region of flanking nucleotides crosses the start or end of the sequence, no output is given for this codon\&. Default value: 100
.RE
.SS "Output section"
.PP
\fB\-outseq\fR \fIseqoutall\fR
.RS 4
.RE
.SH "BUGS"
.PP
Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
.SH "SEE ALSO"
.PP
getorf is fully documented via the
\fBtfm\fR(1)
system\&.
.SH "AUTHOR"
.PP
\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
.RS 4
Wrote the script used to autogenerate this manual page\&.
.RE
.SH "COPYRIGHT"
.br
.PP
This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
.sp
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