[DAS2] ids to coordinates?

[Steve Chervitz]

Ann,

Here's my response from a similar question you asked last May:
http://lists.open-bio.org/pipermail/das2/2006-June/000735.html

The example URLs I gave for the Affymetrix DAS/2 server no longer work (not
implemented -- but Gregg is planning to fix this in the near future).

For now I'd recommend using the biopackages server. Example:
http://das.biopackages.net/das/genome/human/17/feature?name=ACTA1

You can include multiple name=XXX parameters in the query to retrieve data
for all gene names in the same response document (multiple feature filters
with the same name are OR'd together, as described here:
http://biodas.org/documents/das2/das2_get.html#feature_filters ).

Cheers,
Steve

> From: Ann Loraine <aloraine at gmail.com>
> Date: Thu, 11 Jan 2007 13:05:36 -0600
> To: DAS/2 <DAS2 at lists.open-bio.org>
> Subject: [DAS2] ids to coordinates?
> 
> Greetings all,
> 
> Sorry if I already asked this and spaced on the answer...
> 
> Can I give a DAS2 server (and if yes, which one?) a list of HUGO gene
> names and then get back the start and end coordinate of the gene on
> hg17? (Note: the current version is hg18.)
> 
> I'm doing a candidate gene-based population genetics project, and I
> need to be able to quickly get back the boundaries of a bunch of genes
> (as determined in the usual way, e..g, cDNA-to-genome alignments)
> where I have the HUGO name but that's it.
> 
> I think maybe Lincoln mentioned something like this was available via
> a site at CSHL, or maybe Hapmap?
> 
> I think it would be pretty nifty if the nicely-funded Hapmap project
> could provide such a service, if it does not already :-)
> 
> Yours,
> 
> Ann
> 
> -- 
> Ann Loraine
> Assistant Professor
> Departments of Genetics, Biostatistics,
> and Computer Information Sciences
> University of Alabama at Birmingham
> http://www.transvar.org
> 205-996-4155
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