[BioC] How do you find your orthologues?

[Karl Brand]

Bruce, Hans, Alex,

Many thanks for the tips and the example.

Both biomaRt and HomoVert look excellent to map across species. But, and 
i could be wrong, i could be out of luck for for a direct mapping 
to/from GI numbers.

I'll either be back with a solution. Or a new thread :)

Thanks again,

Karl


On 26/06/12 12:47, Bruce Moran(External) wrote:
> Hi Karl,
>
> biomaRt is great for this:
>
> http://www.bioconductor.org/packages/2.2/bioc/vignettes/biomaRt/inst/doc
> /biomaRt.pdf
>
> Pretty nice walkthroughs in the manual above too.
>
> Good luck,
>
> Bruce.
>
> -----Original Message-----
> From: bioconductor-bounces at r-project.org
> [mailto:bioconductor-bounces at r-project.org] On Behalf Of Karl Brand
> Sent: 26 June 2012 11:43
> To: bioconductor at r-project.org
> Subject: [BioC] How do you find your orthologues?
>
> 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