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.

COPYRIGHT

       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.