[ensembl-dev] Restricting species considered for ortholog requests

[Javier Herrero]

Hi Jason

You can use the HomologyAdaptor 
(http://www.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1DBSQL_1_1HomologyAdaptor.html) 
to get these relationships. You can try either the 
fetch_all_by_Member_paired_species or the 
fetch_all_by_Member_paired_species methods. For instance,

$homology_adaptor->fetch_all_by_Member_paired_species($hsap1_member, 
"mus_musculus", "ENSEMBL_ORTHOLOGUES");

will return [$mmus1_member], and

$homology_adaptor->fetch_all_by_Member_paired_species($hsap2_member, 
"mus_musculus", "ENSEMBL_ORTHOLOGUES");

will return [$mmus2_member, $mmus2'_member]. If you want to get the 
intra-species paralogues as well, you can add:

$homology_adaptor->fetch_all_by_Member_paired_species($hsap2_member, 
"homo_sapiens", "ENSEMBL_PARALOGUES");

I hope this helps

Javier

On 12/02/12 01:24, Jason Merkin wrote:
> Hello. I am trying to identify duplications that have occured within a 
> group of species. I have gone through the tutorial and the mailing 
> list archives and couldn't find anything on it. I will use the example 
> on the webpage that explains the homology definitions 
> (http://ensembl.genomics.org.cn:8058/info/docs/compara/homology_method.html) 
> to illustrate what I am trying to do. Using just human and mouse, as 
> on the diagram, I would like to query with Hsap1 and get the set of 
> (Hsap1, Mmus1); query with Hsap2 and get (Hsap2, Hsap2', Mmus2, 
> Mmus2'); and query with Hsap3 and get (Hsap3, Mmus3, Mmus3'). Is there 
> a way to specify the homology type and, more importantly, restrict the 
> species to be considered for definining the homology?
>
> Thanks for any help,
> Jason Merkin
>
>
>
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-- 
Javier Herrero, PhD
Ensembl Coordinator and Ensembl Compara Project Leader
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge - CB10 1SD - UK

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