[BioC] How do you find your orthologues?

[Karl Brand]

Esteemed Bioconductor UseRs and Devs,

How do you find your orthologues?

We have a variety of data (proteomic, expression) from a variety of 
species (mouse, rat, pig, human) with lots of primary identifiers 
(GI-number, ensembl gene ID, gene-symbol). What we need to do is take 
such an identifier, say a mouse ensembl gene ID, and have a list of 
identifers for the mapped orthologue (to say rat and pig) returned. It 
seems compara will do this, via a Perl API

http://www.ensembl.org/info/docs/api/compara/index.html

Can it also be accessed via R/BioConductor? WHich package? BiomaRt? Or 
is there another BioConductor package employed for this task i should be 
looking at?

With thanks in advance for tips and reflections before i spend another 
day hunting for a package to achieve this,

Karl


-- 
Karl Brand
Dept of Cardiology and Dept of Bioinformatics
Erasmus MC
Dr Molewaterplein 50
3015 GE Rotterdam
T +31 (0)10 703 2460 |M +31 (0)642 777 268 |F +31 (0)10 704 4161