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

[Matthew Pocock]

Hi David,

There is a server at http://servlet.ensembl.org/das/ that serves 
transcripts (currently an ensembl transcript is nearly equivalent to an 
EMBL CDS). You can translate this if you wish by using the magic:

SymbolList translation =
  RNATools.translate(
   RNATools.transcribe(
    transcript.getSymbols()));

where transcript is any transcript feature. You should be able to find 
transcript features by doing something like:

FeatureHolder transcripts = chr.filter(
   new Filter.ByType("transcript),
   true // recurses through tree
);

Of course, this will find all transcripts on an entire chromosome which 
will be expensive, but you get the idea.

Matthew

Dr S.M. Huen wrote:

> On Sat, 19 May 2001, Dr S.M. Huen wrote:
> 
> 
>> 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!
>> 
> 
> I've got some progress now that I finally use the right version of the DAS
> protocol.  From the stylesheet, it looks as if no translation info is
> available from this server.  Does anyone know another DAS server
> compatible with the biojava DAS client that I could get translation info
> from?
> 
> Thanks,
> David Huen
> 
> 
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