Question: How do you find your orthologues?
7.5 years ago by
k. brand • 420
k. brand • 420 wrote:
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
ADD COMMENT • link •