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

[Javier Herrero]

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