[ensembl-dev] Protein Sequence
jherrero at ebi.ac.uk
Fri Jun 22 10:00:12 BST 2012
Bert is right, the protein sequences are not stored in the core database. However you can find a copy of all proteins in Ensembl in the compara database. We need them in the compara database in order to speed up the retrieval of protein sequences from all species at once.
Have a look at the member and sequence tables.
I hope this helps
Sent from my Kindle Fire
From: Bert Overduin <bert at ebi.ac.uk>
Sent: Fri Jun 22 10:20:30 GMT+02:00 2012
To: Ensembl developers list <dev at ensembl.org>
Subject: Re: [ensembl-dev] Protein Sequence
No, protein sequences are generated on the fly.
On Fri, Jun 22, 2012 at 8:54 AM, Stuart Meacham <sm12 at sanger.ac.uk> wrote:
> Is the Protein Sequence retreived by, for example,
> $transcript->translate()->seq() held in a particular table in the DB? I had
> a root around Core and couldn't find anything obvious.
> Dev mailing list Dev at ensembl.org
> List admin (including subscribe/unsubscribe):
> Ensembl Blog: http://www.ensembl.info/
Bert Overduin, Ph.D.
Vertebrate Genomics Team
EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
Ensembl browser: http://www.ensembl.org
Mailing lists: http://www.ensembl.org/info/about/contact/mailing.html
Dev mailing list Dev at ensembl.org
List admin (including subscribe/unsubscribe): http://lists.ensembl.org/mailman/listinfo/dev
Ensembl Blog: http://www.ensembl.info/
-------------- next part --------------
An HTML attachment was scrubbed...
More information about the Dev