[ensembl-dev] fetch all within species paralogous genes

[Matthieu Muffato]

Dear Shaohua

The most efficient way is probably to use the fetch_all_by_MethodLinkSpeciesSet_orthology_type() method from the HomologyAdaptor

You first have to create a MethodLinkSpeciesSet object
my $mlss_adaptor = $reg->get_adaptor("Multi", "compara", "MethodLinkSpeciesSet");
my $mlss = $mlss_adaptor->fetch_by_method_link_type_registry_aliases("ENSEMBL_PARALOGUES", ["human"]);
This object describes which kind of data you want, and on which species

Then, you can retrieve the homologies:
my $homology_adaptor = $reg->get_adaptor("Multi", "compara", "Homology");
my $all_paralogues = $homology_adaptor->fetch_all_by_MethodLinkSpeciesSet_orthology_type($mlss, "within_species_paralog");

This method can be extended to orthologues and to pairs of species. It is the fastest when it comes to fetch big sets of homologues

Hope this helps,
Matthieu

On 17/04/12 10:45, shaohua fan wrote:
> Dear all,
> 
> As a newbie of Ensembl compara API, I want to ask whether there is a way to fetch all the within species paralogous genes of one specified genome by using the compara API? I have searched the former emails and Ensembl website and only found the solution for the single gene in the tutorial of compara API.
> 
> Thanks a lot!
> 
> shaohua