[ensembl-dev] Converting Uniprot IDs to ensembl ID

[Patrick Meidl]

On Mon, Nov 28 2011, James Blackshaw <jab250 at mrc-mbu.cam.ac.uk> wrote:

> I've been trying to convert some large (~70 000) lists of
> identifiers from Uniprot accession numbers to their relevant Ensembl
> IDs.

in my experience the fastest way to achieve this is to download the ID
mapping file from the latest Uniprot release (called idmapping.txt IIRC)
and use this file to do the mapping (requires a few lines of perl to
read the relevant mappings into your script).

    patrick

-- 
Patrick Meidl, Mag.
Bioinformatician

Ce-M-M-
Research Centre for Molecular Medicine
of the Austrian Academy of Science

Lazarettgasse 14 / AKH BT 25.3
Vienna, Austria

room 02.205
phone +43 1 40160 70016
email pmeidl at cemm.oeaw.ac.at
web http://www.cemm.at/