getorf - Finds and extracts open reading frames (ORFs)
getorf -sequence seqall
[-table list]
[-minsize integer]
[-maxsize integer]
[-find list]
-methionine boolean
-circular boolean
-reverse boolean
-flanking integer
-outseq seqoutall
getorf -help
getorf is a command line program from EMBOSS (“the
European Molecular Biology Open Software Suite”). It is part of the
"Nucleic:Gene finding" command group(s).
-table list
-minsize integer
Default value: 30
-maxsize integer
Default value: 1000000
-find list
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.
-methionine boolean
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
-circular boolean
Default value: N
-reverse boolean
Set this to be false if you do not wish to find ORFs in
the reverse complement of the sequence. Default value: Y
-flanking integer
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
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).
getorf is fully documented via the tfm(1) system.
Debian Med Packaging Team
<debian-med-packaging@lists.alioth.debian.org>
Wrote the script used to autogenerate this manual
page.
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.