Orthology Search-Rbh Or Biomart

Question

[jackuser1979]

I have set of genes of interest(in Ensembl gene ids), I want to compare with five closely related species in Ensembl and to find orthologues of genes among all. I have plan to go for reciprocal blast(RBH) or using Ensembl-Biomart. Which is the best method to find orthologues?

Answer 1

[Andrzej Zielezinski]

Use RoundUp2.0, the largest database (1800 genomes) of orthologs.

The orthologs are computed using the Reciprocal Smallest Distance (RSD) algorithm that is more accurate than standard reciprocal best blast strategy.

Answer 2

[JC]

Why not to use Ensembl-Compara? http://ensembl.org/info/docs/compara/index.html

[jackuser1979]

I am a biologist. It is difficult for me to setup Compara Perl API Installation.

[JC]

I have used it before, let me know if you need some help.