How To Find Yeast Homolog?

Question

[guhchengzi]

Hi, I have a list of hundreds of genes from various species. Is there a way to find yeast homologs of these gene. Either cerevisiae or pombe will do.

[Jason]

How many species are you talking about that make up the "hundreds of genes"?

[guhchengzi]

The genes come from about 50 different species. I am looking for a kind of post translational modification. And I have a list of proteins from all the mass spec data exist. I want to find yeast homologs of these proteins.

Answer 1

[SES]

Depending on exactly what type of data you want, some good places to start are Ensembl (link to tutorial) or the OrthoMCL database of protein clusters. If you want to try and infer ortholog/paralog relationships, Ensembl will be more appropriate though, OrthoMCL may have a larger coverage of the species you are interested in (and this may be appropriate if you just want to find homologous genes by similarity).

[guhchengzi]

Thanks you. I know how to find homologous gene individually using ensemble. But in terms of hundreds of genes, it will be annoying to find individually. So I am asking if there is a way to submit a list of genes from different species to find yeast homolog.

[SES]

It was not clear what you were asking in your question because you just said you are trying to find homologous genes. If you don't want to search individually, I would recommend using the Compara API if you want to get homolgous proteins or alignments.