[DAS] Human DAS Servers

Thomas Down td2@sanger.ac.uk
Sat, 15 Dec 2001 09:50:55 +0000


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 :-).