Deano <rilecode at no_spamchemist.com> wrote:
> I have several thousand sequences that I would like to determine the
> longest open reading frame on and then output the AA sequence of that
> ORF while hopefully maintaining the affiliation with the original
> accession number. All of the ORF prediction programs I have found are
> set up to do one at a time. I am not asking for perfection in the
> predictions just speed in the processing. Does anyone have
> suggestions on how to do this?
You might want to have a look at EMBOSS:
This is a suite of command-line programs. There is a tool called getorf that
extracts open reading frames for you. Most EMBOSS tools can handle multiple
sequences. If you have trouble you can still call getorf from a little script...
Dr. Philipp Pagel
Department of Cellular and Molecular Physiology phone: (203) 785-6835
Yale University fax: (203) 785-4951
New Haven, CT 06520, USA