[Bioperl-l] ensembl modules

Ewan Birney birney at ebi.ac.uk
Sun Aug 22 09:45:53 EDT 2004

On Sun, 22 Aug 2004, Yin Yanbin wrote:

> Hello,
> How can I use Refseq protein IDs or UniProt IDs or GenBank IDs to
> extract the corresponding Ensembl genes?

the best thing is to check on Mart at


Then select "human, Ensembl genes" as a focus, unselect the genome
restriction on the filter (so it is genome wide) and select the ID-filter,
using RefSeq IDs. Then in output you can get all manner of outputs.

If you want to write a program, then using either the Ensembl APIs - for a
starting point look


in either Java or Perl will work or try out the Mart Java API and
command-line "shell"


Finally you can you MySQL drivers directly against ensembldb.ensembl.org
if these APIs are not to your taste.

If you get stuck, do get in touch with our helpdesk at:


> Thanks!
> Yanbin
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