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

[Ann Loraine]

Hi Steve,

Thank you very much for the info!

Now I have another question...

I'd like to look up the genomic coordinates of a list of mouse genes
using their numeric Entrez Gene ids.

If it's not too much bother, do you think you'd be able to give me
some tips on how to do this using DAS?

btw, the DAS services have been hugely helpful to me in the last week.
We have already found some interesting results with minimal coding.
And the coding was actually fun because there was NO SCREEN-SCRAPING.
Pure bliss.

-Ann

On 5/16/06, Steve Chervitz <Steve_Chervitz at affymetrix.com> wrote:
> 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
>
>


-- 
Ann Loraine
Assistant Professor
Section on Statistical Genetics
University of Alabama at Birmingham
http://www.ssg.uab.edu
http://www.transvar.org