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.

Sequence Analysis in a Nutshell
Sequence Analysis in a Nutshell: A Guide to Common Tools and Databases
ISBN: 059600494X
EAN: 2147483647
Year: 2005
Pages: 312

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