[ensembl-dev] Source of refseq data in otherfeatures

[Thibaut Hourlier]

Hi Reece,
Just to add to RIshi's answer; only the sequences from RefSeq which align the genome of interest are stored in the otherfeatures database

Thanks
Thibaut

On 4 Jun 2013, at 14:26, Rishi Nag <rn6 at sanger.ac.uk> wrote:

> On Tue, 04 Jun 2013 02:22:29 +0100, Reece Hart <reece at harts.net> wrote:
> 
> What's the source of the refseq data in otherfeatures? 
> 
> How current is the otherfeatures data?
> 
> The date of the last release is stored in the otherfeatures meta table with meta_key genebuild.last_otherfeatures_update 
> 
> Typically the db_version in the analysis table should record the refseq version being used for the data. However, this may not have been captured for older releases. Data are downloaded from the NCBI website.
> 
> What reconciliation is done when there are substitutions (e.g., VHL, TNFRSF10C, SERPINE2) or indels (NEFL, ABO, ZAN) in the transcript relative to GRCh37?
> 
> Thanks,
> Reece
> 
> 
> 
> 
> --
> Rishi Nag
> Ensembl Genebuilder
> Wellcome Trust Sanger Institute
> http://ensembl.org
> 
> Using Opera's mail client: http://www.opera.com/mail/
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20130604/b2a35e74/attachment.html>