[DAS] Re: Protein DAS and C. elegans

Julian Gough gough at stanford.edu
Sat May 24 07:47:14 EDT 2003


this is indeed what I am doing, and I very much welcome the move to
modify the spec to allow this explicitly (from what I can make out it
isn't disallowed anyway). 
However I feel that I have to make absolutely clear what Tony said about
it because I think I have been ever so slightly misunderstood. So far as
I can recall from what Tony said no other Protein DAS server is doing
this, only mine, but he said "We routinely use same IDs to 'link'
features into a structure.... If Ensembl encounters a list of exon
features all with the same ID it groups them into a transcript." I think
perhaps referring to non-protein DAS.

Anyway I'm sure you'll get the full story from him.


On Sat, 2003-05-24 at 07:18, Lincoln Stein wrote:
> Hi Tony,
> Julian tells me that the various protein DAS servers are serving domains that 
> are on discontinuous regions of the genome by giving each feature the same 
> feature ID rather than linking them by using the same group.  This strategy 
> makes sense, and is in fact what the GFF3 spec calls for, but isn't what the 
> DAS/1 spec says.  The question is:
> 	- How widespread is this practice?  Should I modify the 1.X spec
> 	retrospecticely to allow it?
> Lincoln
> -- 
> ========================================================================
> Lincoln D. Stein                           Cold Spring Harbor Laboratory
> lstein at cshl.org			                  Cold Spring Harbor, NY
> ========================================================================
Julian Gough
Department of Structural Biology
School of Medicine, Fairchild bldg D109
Stanford University, CA 94305-5126, U.S.A.
Tel: +1 650 7250754
Fax: +1 650 7238464

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