[ensembl-dev] Choosing which protein to do ortholog compare

[Southan, Christopher]

Is there any step in the Compara system that can check the
UniProt-SwissProt (manual curation of the longest ORF) against the CCDS
and or what you select for the Ortholgue assignments ?

Yours, Chris 


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-----Original Message-----
From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf
Of Javier Herrero
Sent: den 28 juli 2011 16:37
To: dev at ensembl.org; Richard Chirko
Subject: Re: [ensembl-dev] Choosing which protein to do ortholog compare

Dear Dick

We generally use the longest protein, but we favour the CCDS entries. In
the 
case of Adamts9 gene, the longest protein product is not part of the
CCDS 
while the second longest is. In those case, we choose the CCDS entry.

I hope this helps

Javier

On Thursday 28 Jul 2011 15:01:23 Richard Chirko wrote:
> Mouse gene Adamts9 shows 2 protein products. One is 1931 AA and the
other
> is 1350 AA. When I click on the Orthologues link, all the comparisons
are
> to the 1350 product. Yet virtually all the proteins they are compared
to
> are in the 1800 to 1950 range. How do you choose which protein product
to
> use for the comparison and is there a way to get (from your site) the
> orthologues for the 1931 AA product? 
> Many thanks for your help in this.
>  
> Dick

-- 
Javier Herrero, PhD
Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK

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