[BioC] Orthologs search

[Sean Davis]

Adrienne,

Have you looked at using biomaRt?  It queries the Ensembl Mart database and 
has a couple of functions (getXref, getHomolog) that you might find useful. 
Here is a link to the vignette.  The two functions of interest are near the 
end of the vignette.

http://www.bioconductor.org/repository/devel/vignette/biomaRt.pdf

Sean

----- Original Message ----- 
From: "Jamain, Adrien J" <adrien.jamain at imperial.ac.uk>
To: <bioconductor at stat.math.ethz.ch>
Sent: Tuesday, June 21, 2005 4:51 AM
Subject: [BioC] Orthologs search


> Dear BioC people,
>
> I'm looking for orthologs of a certain list of genes (mouse => yeast).
> I was trying to do it in an automated way thanks to BioC.
>
> Since I couldn't find any for the particular list, I looked for all
> orthologs (mouse => yeast).
> And I only found 38.
>
> The code chunk below is almost identical to that in the homology
> vignette, so I suppose it's ok.
>
> Is it normal that I found so few?
>
> Cheers,
> Adrien
>
> Quality control information for  mmuhomology
> Date built: Created: Sun May 15 12:41:11 2005
> ------------------------------------------------------------------------
> --------------------------------------
>> temp = mget(mmuhomologyHGID, mmuhomologyDATA)
>> tempFun = function(x) {
> for (i in x) {
> if (!is.na(i[["homoOrg"]]) && i[["homoOrg"]] == "sce") {
>    return(i)
> }
>    return(NA)}
> }
>> goodGenes = sapply(temp, tempFun)
>> goodGenes = goodGenes[!is.na(goodGenes)]
>> length(goodGenes)
> [1] 38
>
>
> [[alternative HTML version deleted]]
>
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