checktrans reads a protein sequence containing stops and writes a report of any open reading frames greater than a minimum size. The input sequence is typically produced by transeq.

Here is a sample session with checktrans, using the output from a transeq run:

% transeq embl:paamir paamir.pep -auto
% checktrans
Input sequence: paamir.pep
Minimum ORF Length to report [100]: 30
Output file [paamir_1.checktrans]:
Output sequence [paamir_1.fasta]:

Mandatory qualifiers:

[-sequence] (seqall)

Sequence database USA.

-orfml (integer)

Minimum ORF Length to report.

[-report] (outfile)

Output filename.

-outseq (seqoutall)

Sequence file to hold output ORF sequences.

Advanced qualifiers:

-featout (featout)

File for output features.