? Program for batch ORF prediction

philipp.pagel at cmp.yale.edu philipp.pagel at cmp.yale.edu
Thu Sep 13 03:34:48 EST 2001


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:

http://www.uk.embnet.org/Software/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...

cu
	Philipp

-- 
Dr. Philipp Pagel
Department of Cellular and Molecular Physiology        phone: (203) 785-6835	
Yale University                                        fax:   (203) 785-4951
New Haven, CT 06520, USA





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