[Biojava-l] servlet.sanger.ac.uk DAS server

[Thomas Down]

On Sat, May 19, 2001 at 11:15:03PM +0100, Dr S.M. Huen wrote:
> I've implemented a preliminary version of a feature renderer that is
> capable of rendering CDSs across a six-translation frame display.
> 
> Howver I have some grave problems in getting any suitable input for it.
> What is the annotation type used to filter for the coding region of a
> region at the Sanger server?  I've tried 'CDS' without success.
> 
> I don't know the DAS protocol well enough to to use wget to get this info
> as my attempts just result in the server getting puzzled with me!

No, the CDS information isn't currently there.  This is
a deficiency in biojava-ensembl: it only exposes ensembl
transcripts, rather than the coding regions (which may
be sub-portions of the transcript).  This came about because
versions of ensembl < 1.00 didn't include any untranslated portions
of transcripts, so the transcript object effectively WAS the
CDS.  This is now at the top of my todo list, and will get
done as soon as I've finished preparations for a presentation
I have to give tommorow.

Thanks,

   Thomas.