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

Michael Paulini mh6 at sanger.ac.uk
Thu Jul 28 15:48:06 BST 2011

I think compara nowadays just uses whatever has been set as 
representative transcript in the respective core databases.
So you can easily roll your own script to set that to whatever 
transcript you want.


On 28/07/11 15:43, Southan, Christopher wrote:
> 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
> 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

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