[BioC] How do you find your orthologues?

[James W. MacDonald]

Hi Karl,

You might also look at the hom.Xx.inp.db packages, which map orthologues 
via InParanoid. There is a convenience function inpIDMapper() in 
AnnotationDbi that does the mappings. Or you could have some SQL fun and 
do your own ;-D

Best,

Jim



On 6/26/2012 12:20 PM, Karl Brand wrote:
> 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
>>
>>
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099