Good ORF Finder?

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


>        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

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:


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

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