xenial (1) getorf.1e.gz

Provided by: emboss_6.6.0+dfsg-3build1_amd64 bug

NAME
       getorf - Finds and extracts open reading frames (ORFs)


SYNOPSIS
       getorf -sequence seqall [-table list] [-minsize integer] [-maxsize integer] [-find list]
              -methionine boolean -circular boolean -reverse boolean -flanking integer -outseq seqoutall

       getorf -help


DESCRIPTION
       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).


OPTIONS
   Input section
       -sequence seqall

   Additional section
       -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.

   Advanced section
       -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

   Output section
       -outseq seqoutall


BUGS
       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).


SEE ALSO
       getorf is fully documented via the tfm(1) system.


AUTHOR
       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.