getorf - Finds and extracts open reading frames (ORFs)

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       the EMBOSS developers (http://sourceforge.net/tracker/?group_id=93650&atid=605031).

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EMBOSS 6.4.0                                       05/11/2012                                         GETORF(1e)

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).

       getorf - Finds and extracts open reading frames (ORFs)

Inputsection-sequenceseqallAdditionalsection-tablelist-minsizeinteger
           Default value: 30

       -maxsizeinteger
           Default value: 1000000

       -findlist
           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.

   Advancedsection-methionineboolean
           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

       -circularboolean
           Default value: N

       -reverseboolean
           Set this to be false if you do not wish to find ORFs in the reverse complement of the sequence.
           Default value: Y

       -flankinginteger
           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

   Outputsection-outseqseqoutall

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

getorf-sequenceseqall [-tablelist] [-minsizeinteger] [-maxsizeinteger] [-findlist]
              -methionineboolean-circularboolean-reverseboolean-flankinginteger-outseqseqoutallgetorf-help