[Bioperl-l] ensembl modules

[Ewan Birney]

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

http://www.ensembl.org/Multi/martview

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

http://www.ensembl.org/Docs/

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

http://www.ebi.ac.uk/biomart/index.html

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:

http://www.ensembl.org/helpdesk/







>
> Thanks!
>
> Yanbin
>
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