How To Get Orthologous Gene Id For Another Specie Without Alignment?

Question

[GAO Yang]

Hi~ I know that I can retrieve the ID of possible orthologous genes between two species by BioMart. For example, if I set the "dataset" as specie A, and "filter" as Orthologous Specie B Genes. The gene IDs of all possible orthologous in specie A will return.

But what i want to do is slightly different here. I have a list of ensemble genes IDs of takifugu (pufferfish), about 900. Now I need the orthologous gene ID of another specie which are corresponding to these genes in list. Is there any way to do it without alignment such as blast ?

Thanks for your opinion and suggestion !

Answer 1

[JC]

Use the Compara API http://uswest.ensembl.org/info/docs/api/compara/compara_tutorial.html

[GAO Yang]

This way can do. Thanks, JC. But maybe due to the net speed, my script can't reach a fine results often. I'd better stick to the biomart way to do it. Anyway, thanks for your help :)

Answer 2

[karolos.chapple]

I have recently discovered metaPhOrs. They have a very good Python API available on request. As far as I know they can only deal with UniProt IDs but if you can map your ensembl IDs to UniProt you can batch query metaPhOrs.