ESTs, ORFs and curated databases

Gary Williams gwilliam at hgmp.mrc.ac.uk
Wed Mar 14 11:09:01 EST 2001


In article <98j347$1vu$1 at niobium.hgmp.mrc.ac.uk>,
Alan Bleasby <ableasby at hgmp.mrc.ac.uk> wrote:
>In article <15020.40008.691662.957167 at chevrotain.mips.biochem.mpg.de>,
>	rudd at mips.biochem.mpg.de (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 embnet.org 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.

http://www.ch.embnet.org/software/ESTScan.html

Source: http://www.isrec.isb-sib.ch/ftp-server/ESTScan/

This should do what he requires.

Gary

Gary Williams               Tel: +44 1223 494522  Fax: +44 1223 494512
mailto:G.Williams at hgmp.mrc.ac.uk            http://www.hgmp.mrc.ac.uk/
Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK






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