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getorf(1e)


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.



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