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/ins t/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