[Bioperl-l] how to get annotations (especially ensembl IDs) for a list of genes?

[Sendu Bala]

zhihua li wrote:
> Hi all,
> 
> I have a list of like 300 genes (actually their refseq IDs).  Now I 
> wanna get more information (annotations) for each of the genes. 
> Speficially, I want a mapping of the refseq IDs to Ensembl gene IDs.
> 
> I know how to do it through a web page. But I'm wondering if I can also 
> do it via bioperl

One possible way is to use the Ensembl perl API:
http://www.ensembl.org/info/software/core/core_tutorial.html

You'd get a gene or transcript adapator and use
fetch_all_by_external_name() iirc.

I'm aware that not every entrez id can be mapped that way, but perhaps
most if not all refseqs will work.