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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).


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

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