Question: Orthology Search-Rbh Or Biomart
0
gravatar for jackuser1979
7.5 years ago by
jackuser1979870
US
jackuser1979870 wrote:

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?

ADD COMMENTlink written 7.5 years ago by jackuser1979870
5
gravatar for a.zielezinski
7.5 years ago by
a.zielezinski9.0k
a.zielezinski9.0k wrote:

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.

ADD COMMENTlink written 7.5 years ago by a.zielezinski9.0k
1
gravatar for JC
7.5 years ago by
JC9.5k
Mexico
JC9.5k wrote:

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

ADD COMMENTlink modified 7.5 years ago by Istvan Albert ♦♦ 82k • written 7.5 years ago by JC9.5k

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

ADD REPLYlink written 7.5 years ago by jackuser1979870

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

ADD REPLYlink written 7.5 years ago by JC9.5k
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