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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