getorf finds and outputs the sequences of open reading frames (ORFs).

Here is a sample session with getorf:

% getorf -minsize 300
Input sequence: embl:eclaci
Output sequence [eclaci.orf]:

Mandatory qualifiers:

[-sequence] (seqall)

Sequence database USA.

[-outseq] (seqoutall)

Output sequence(s) USA.

Optional qualifiers:

-table (menu)

Code to use. See the fuzztran description for codes.

-minsize (integer)

Minimum nucleotide size of ORF to report.

-find (menu)

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 may be a region that is free of STOP codons or it may be a region that begins with a START codon and ends with a STOP codon. The last three options are probably only of interest to those who want 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 qualifiers:

-[no]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.

-circular (boolean)

Is the sequence circular?

-[no]reverse (boolean)

Set this to be false if you do not want to find ORFs in the reverse complement of the sequence.

-flanking (integer)

If you chose an option in the type of sequence to find that provides the flanking sequence around a STOP or START codon, this allows you to set the number of nucleotides on 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.