[DAS] Human DAS Servers

[Lincoln Stein]

Bio::Das doesn't do the automatic coordinate munging.  The new version 
(Bio-Das2) is supposed to, but currently it's broken.

Bio::DB::GFF does coordinate mapping, but not for DAS servers (it's waiting 
for me to get Bio-Das2 fixed).

Lincoln

On Saturday 15 December 2001 04:50, Thomas Down wrote:
> Hi...
>
> On Sat, Dec 15, 2001 at 03:11:52AM -0500, Cheung, Foo wrote:
> > which other Human DAS Servers can I query by chromosomal coordinates?
>
> About the only things we serve in chromosome coordinates from
> sanger (other than the assembly itself) are karyotype bands.
>
> > which Human DAS Servers requires other coordinates for querying? and what
> > are those? contigs? karyotypes?
>
> Most of the Ensembl-DAS information is served in raw-contig
> coordinates.  A few things in FPC contig coordinates.  And
> SNPs on clones.
>
> I don't know of anything which is served on karyotype bands.
> Currently these aren't being served as componentFeatures, so
> they're not annotatable.
>
> > I suspect some of them require querying by contigs and karyotype and I
> > will have to do a coordinate translation system on the fly to convert
> > chromo coordinates.
> > Is there any code kicking around that does this?
> > Is Bio::DB::GFF the way to go on this?
>
> How about the BioJava DAS client?  It's been a part of the
> BioJava core for a while now, and allows you to handle DAS
> data just like any other datasource:
>
>    SequenceDB das = new DASSequenceDB(new URL("blah..."));
>    Sequence seq = das.getSequence("chr22");
>    FeatureHolder features_in_my_favourite_region = seq.filter(
>        new FeatureFilter.OverlapsLocation(
>            new RangeLocation(start, stop)
>        ), true
>    );
>
> This automagically walks the assembly and fetches everything
> you need.  Made the das client application easy to write :-).
>
>
>       Thomas.
> _______________________________________________
> DAS mailing list
> DAS@biodas.org
> http://biodas.org/mailman/listinfo/das

-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
========================================================================