This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Orthology Search-Rbh Or Biomart

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?

gene-annotation comparative-genomics
• 3,591 views • link
updated by Ram Ram • written by jackuser1979 jackuser1979

2 answers

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.

• 2 views • link
written by Andrzej Zielezinski Andrzej Zielezinski

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

• 0 views • link
updated by Istvan Albert Istvan Albert • written by JC JC

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

• 0 views • link
written by jackuser1979 jackuser1979

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

• 0 views • link
written by JC JC

Log in to answer this question.

More posts like this