Question: How To Get Orthologous Gene Id For Another Specie Without Alignment?
1
gravatar for GAO Yang
7.4 years ago by
GAO Yang250
GAO Yang250 wrote:

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 !

sequence • 3.4k views
ADD COMMENTlink written 7.4 years ago by GAO Yang250
0
gravatar for JC
7.4 years ago by
JC9.4k
Mexico
JC9.4k wrote:

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

ADD COMMENTlink written 7.4 years ago by JC9.4k

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 :)

ADD REPLYlink written 7.4 years ago by GAO Yang250
0
gravatar for karolos.chapple
7.4 years ago by
karolos.chapple0 wrote:

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.

ADD COMMENTlink written 7.4 years ago by karolos.chapple0
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