[DAS] Finding the ADAM2 Gene via Ensembl DAS

[Ethan Cerami]

Thomas,

Thanks (as always).  So, in order to recreate the
Nature example, I first need to map the gene
chromosome location to its contig.  Then, request
features for that contig.  

ADAM2 and ADAM18 are actually on different contigs. 
So, I was eventually able to track down both genes.

Ethan

--- Thomas Down <thomas@derkholm.net> wrote:
> Once upon a time, on a computer far far away, Ethan
> Cerami wrote:
> > 
> > First some overview:  if you click on this link:  
> >
>
http://www.ensembl.org/Homo_sapiens/contigview?highlight=&chr=8&vc_start=38800000&vc_end=39190000&x=0&y=0,
> > in the detailed panel on the bottom, you will see
> two
> > known genes, ADAM18 and ADAM2.
> > 
> > I am trying to get this same gene data out of
> Ensembl
> > via DAS.  I tried several Ensembl data sources,
> > including:  ensembl930, ens_ncbi30refseq
> > (Ensembl-mapped Human RefSeqs), ens930cds (Ensembl
> > CDS).  I finally tried ens_ncbi30trans (NCBI
> > Transcripts).  Here's the query I sent:
> > 
> >
>
http://servlet.sanger.ac.uk:8080/das/ens_ncbi30trans/features?segment=8:38800000,39190000
> > 
> > In the response, I got back 14 features, all named
> > ADAM2, but each one is located at a different
> > location.
> >
> > So, my questions:
> > 
> > 1.  Am I using the right Ensembl data source?
> 
> No, I don't believe that you are.  The source you're
> looking
> at is an NCBI genebuild, which I don't think can be
> expected
> to be the same as Ensembl.
> 
> The core Ensembl data (including gene predictions)
> is on
> /das/ensembl930/.  But trying the query you show
> above on
> this datasource isn't going to work... (see below).
> 
> > 2.  Why do I get back 14 ADAM2 Genes, instead of
> just
> > one?
> 
> One for each exon.  The DAS protocol doesn't have
> any way
> to return a single FEATURE element with a
> non-contiguous
> location, so gene structures really have to be
> returned as
> many individual FEATUREs grouped together.  I note
> that
> Ensembl actually predicts 13 exons for ADAM2.  14 is
> close
> enough for me -- maybe NCBI managed to map a bit
> more UTR
> in this case.
> 
> > 3.  Why don't I get back the ADAM18 gene?
> 
> Don't know.  I presume NCBI don't predict it (or,
> possibly,
> put it somewhere else).
> 
> 
> 
> The big issue here is actually that DAS servers
> don't *have*
> to provide you the annotation you want in
> chromosomal coordinates.
> It was implemented in this way so that annotation
> could potentially
> survive across assembly changes.  The Ensembl DAS
> server actually
> choses to serve gene structures in either contig
> coordinates
> (if the whole gene fits) or else supercontig
> coordinates
> (the forthcoming version actually drops the
> supercontigs and
> just has clone, contig, and chromosomal coordinates,
> so this will
> make life slightly easier).
> 
> Secondary issue: the Ensembl DAS server will call
> the gene
> structure ENST00000265708, rather than ADAM2.  This
> is because
> the DAS protocol doesn't (to the best of my
> knowlege) support
> synonyms.  The Ensembl server uses ENST numbers as
> the primary
> ID, on the basis that these are something consistent
> which every
> single prediction has.
> 
> If you actually want to see it directly from
> Ensembl, try:
> 
>   
>
http://servlet.sanger.ac.uk:8080/das/ensembl930/features?segment=NT_034911;type=exon
> 
> A better bet would be to use some dedicated DAS
> client code, such
> as that included in the BioJava library, to access
> this data.
> This will handle all the sequence assembly issues
> for you, so you
> can do:
> 
>     SequenceDB ensemblDAS = new DASSequenceDB(
>        new
>
URL("http://servlet.sanger.ac.uk:8080/das/ensembl930/")
>     );
>     Sequence chr = ensemblDAS.getSequence("8");
>     FeatureHolder someFeatures = chr.filter(
>         new FeatureFilter.OverlapsLocation(
>             new RangeLocation(38800000, 390000000)
>         )
>     );
> 
> And get back what you expect.
> 
>     Thomas.
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