hi Karl,

another possible solution might be the package "HomoVert":

http://labs.fhcrc.org/fero/R/HomoVert.html

that contains a Homologene (NCBI ) conversion table (currently Build 64)
and functions that use this table to convert Entrez Gene IDs from one
species to another.

Alex

On Tue, Jun 26, 2012 at 12:43 PM, Karl Brand <k.brand@erasmusmc.nl> wrote:

> 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<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
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