[DAS2] complex feature examples

Steve Chervitz Steve_Chervitz at affymetrix.com
Fri Aug 18 23:44:05 UTC 2006

Excellent idea Andrew.

> From: Andrew Dalke <dalke at dalkescientific.com>
> Date: Sat, 19 Aug 2006 00:03:50 +0200
> To: DAS/2 <das2 at lists.open-bio.org>
> Subject: [DAS2] complex feature examples
> I would like a dozen or two examples of features - especially
> complex features - in das2xml format.  We discussed this last
> February but it didn't lead to anything.
> I think this would be useful for three reasons:
>    - help make sure our spec works (any last details we forgot?)
>    - provide better examples for the documentation
>    - help new DAS people learn best practices
> Here are a few ideas:
>    exons, blast results, haplotype block for a set of snps,
>     probe sets, primer locations (including cut point?),
>     predicted gene locations, repressor locations

Adding to this: representing different types of alternative splicing. See
this figure:


In the context of DAS, we should be able to deal with alt splicing in two

1) read-only context: representing sets of features belonging to a
transcript that exhibits alt splicing, indicating which features belong to
which variants and that the variants are related.

2) writeback context: being able to add alt splice information about a
transcript which originally lacked any alt splicing information, and to
cover this for the various classes of alt splicing.

That should give the spec a good workout.


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