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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@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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >