[DAS] retrieve genes by name

Maximilian Haeussler maximilianh at gmx.de
Fri Jul 9 17:39:06 EDT 2004


Hi,

I'm a complete newbie to DAS and couldn't find documentation on this issue, so I 
hope you can help me:

1) In june 03 there was a discussion on this list started by Ethan Cerami 
(http://portal.open-bio.org/pipermail/das/2003-January/000647.html) about 
finding a gene by it's (hugo?) name and retrieving the sequence. I didn't 
completely understand it, but from what I've understood, retrieving a CDS was 
not that straigforward. Did it get anything easier in the meantime?

2) I am trying to retrieve genes by locuslink/HUGO or any other IDs from biojava 
and get their 5' sequence. Could you point me to some documentation that 
describes this task? Of course, the best would be some "biojava in anger"-style 
cookbook-like recipe on the internet, but any kind of keyword is appreciated. 
Yes, there is the DAS client in biojava, but it does not seem to support gene 
names. Or am I off the track here, is DAS simply not meant to support searches 
like this directly?

Thanks in advance
Max



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