Good ORF Finder?

Philipp Pagel p.pagel at gsf.de
Fri Feb 21 04:42:39 EST 2003


	Hi!

>        I need a good ORF (Opening Reading Frame) Finder. I am going to
> use the full-length cDNA sequences from MGC and find there corresponding
> proteins. Do you know any good one for this purpose? I am aware of ESTScan
> and the one at NCBI. However, the former probably is an overkill because
> the MGC sequences are supposedly of high quality. The one at NCBI doesn't
> seem to have a Standalone version (if you know where it is, can you
> tell me where to download it?).

You can find ESTscan at http://www.isrec.isb-sib.ch/ftp-server/ESTScan/

If you assume that your sequence is of high quality and you just want to
find all (or the longest) ORF in a sequence I recommend the getorf
program from the EMBOSS suite:

http://www.emboss.org/

cu
	Philipp

-- 
Dr. Philipp Pagel                                Tel.  +49-89-3187-3675
Institute for Bioinformatics / MIPS              Fax.  +49-89-3187-3585
GSF - National Research Center for Environment and Health
Ingolstaedter Landstrasse 1
85764 Neuherberg
Germany
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