ESTs, ORFs and curated databases

Gary Williams gwilliam at
Wed Mar 14 11:09:01 EST 2001

In article <98j347$1vu$1 at>,
Alan Bleasby <ableasby at> wrote:
>In article <15020.40008.691662.957167 at>,
>	rudd at (Stephen Rudd) writes:
>> Bioinformaticians,
>> kindly point me in the right direction ? Tools such as EMBOSS getseq
>> often identify the wrong sequences and the cDNA sequences can be ugly !
>There was a problem with getorf in EMBOSS but that was fixed a couple
>of releases ago. I wasn't aware of any problem with getseq but if
>you have any examples we'd be grateful if you'd email
>emboss-bug at and we'll fix it asap.

It's OK Alan.
I've been talking to him and he says:

"The problem with getorf is one to do with the poor quality of the cDNAs,
not the program.  getorf in many cases pulls out a reasonable ORF, but
one that is not in agreement with BLASTX data."

I've pointed him in the direction of ESTScan:

Iseli C, Jongeneel CV, Bucher P
Proc Int Conf Intell Syst Mol Biol 1999;:138-48
ESTScan: a program for detecting, evaluating, and
reconstructing potential coding regions in EST sequences.


This should do what he requires.


Gary Williams               Tel: +44 1223 494522  Fax: +44 1223 494512
mailto:G.Williams at  
Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK

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