[DAS2] most up-to-date mouse das? (mm7)

[Steve Chervitz]

Hi Ann,

The list address has changed. It's now this: das2 at lists.open-bio.org

As for your question, check out the DAS registry server at the Sanger:

http://das.sanger.ac.uk/registry/

I don't think the registry provides an indication of how current the
annotations on each registered server for a given data source, such as
Entrez Gene. It would be a good piece of data to see, though.

As for the Affymetrix DAS/2 server, the mm7 annotations were last updated on
April 19 2006:

http://netaffxdas.affymetrix.com/das2/sources

The available annotations come from the UCSC server, and derive from the
knownGene, all_mrna, genscan, and refFlat files (called 'refseq' on the das
server). Looks like the knownGene data was last updated by UCSC on 15 Dec
2005:
http://hgdownload.cse.ucsc.edu/goldenPath/mm7/database/

Technical note: The xml:base attribute in the das2xml features document
returned by the Affy DAS/2 server is currently incorrect. It should be

xml:base="http://netaffxdas.affymetrix.com/das2/M_musculus_Aug_2005/features
"

instead of

xml:base="http://127.0.0.1:9021/das2/M_musculus_Aug_2005/features"

This will be fixed in the near future.

Steve

> From: Ann Loraine <aloraine at gmail.com>
> Date: Tue, 16 May 2006 03:52:29 -0500
> To: Steve Chervitz <Steve_Chervitz at affymetrix.com>
> Subject: Fwd: most up-to-date mouse das? (mm7)
> 
> Hi Steve,
> 
> Would you post this to the DAS/2 list for me?
> 
> Sorry to bother you, but for some reason my message didn't appear on the list.
> 
> -Ann
> 
> ---------- Forwarded message ----------
> From: Ann Loraine <aloraine at gmail.com>
> Date: May 15, 2006 3:35 PM
> Subject: most up-to-date mouse das? (mm7)
> To: Andrew Dalke <dalke at dalkescientific.com>, DAS/2 <das2 at portal.open-bio.org>
> 
> 
> Hi!
> 
> I working on a QTL study and need to get all the genes mapping to
> various regions under peaks.
> 
> I have the genomic coordinates for the regions so it should be very
> simple for me to get all accessions (feature ids) underneath those
> regions using DAS.
> 
> My question is: what is the most up-to-date server for mm7?
> 
> Here, of course, is UCSC:
> 
> http://genome.cse.ucsc.edu/cgi-bin/das/mm7/features?segment=chr1:3000000,40000
> 00;type=knownGene
> 
> Ultimately, I'd like to get Entrez Gene ids for the genes under the
> peaks so that I can start sifting through the candidates using GO.
> 
> Any tips would be gratefully accepted!
> 
> All the best,
> 
> Ann
> 
> --
> Ann Loraine
> Assistant Professor
> Section on Statistical Genetics
> University of Alabama at Birmingham
> http://www.ssg.uab.edu
> http://www.transvar.org
> 
> 
> -- 
> Ann Loraine
> Assistant Professor
> Section on Statistical Genetics
> University of Alabama at Birmingham
> http://www.ssg.uab.edu
> http://www.transvar.org