[ensembl-dev] Way to get UniprotKb accession number or name using ensembl Perl API's

[Andreas Kahari]

Hi Päivi,

I wrote a short Perl program that will pull out the associated UniProt
identifiers for a list of Ensembl translation stable IDs (see the
attached file).  You should be able to modify the output (and input) of
that program to suit your needs.

Another way of doing this conversion would be to use BioMart (see the
BioMart link at the top of the Ensembl home page).


Feel free to get back to us if you have further queries.

Cheers,
Andreas

On Mon, Oct 25, 2010 at 12:06:44PM +0300, Päivi Rosenström wrote:
> Hi!
> 
> Is there a way to get the UniprotKb accession number or name using
> ensembl Perl API's ?   I would like to analyze the SNPs  using
> Polyphen-2 but it seems to require UnprotKb accession number and all
> I have is Ensembl protein id's.
> 
> Thanks in advance!
> 
> Päivi
> 
> 
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev
> 

-- 
A n d r e a s K ä h ä r i * E n s e m b l S o f t w a r e D e v e l o p
e r * E u r o p e a n B i o i n f o r m a t i c s I n s t i t u t e ( E
M B L - E B I ) * W e l l c o m e T r u s t G e n o m e C a m p u s * H
i n x t o n C a m b r i d g e C B 1 0 1 S D * U n i t e d K i n g d o m
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Paivi.pl
Type: application/x-perl
Size: 1170 bytes
Desc: not available
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20101025/073eec20/attachment.pl>