[DAS] Displaying protein sequences and features

[Matthew Pocock]

 --- Kris Boulez <kris.boulez at algonomics.com> wrote: >
[ I might make a complete fool of myself by asking
> the following, but
>   anyway ]

There are several like-minded fools who have asked the
same questions :)

> 
> We want to visualize a (set of) protein sequence(s),
> together with the
> features (public together with private ones). The
> way DAS
> clients/servers display stuff is what we also have
> in mind.
> 
> Some questions:
> 
> - How (genomic)DNA based is the concept of DAS ?

In principle, it is not very tied to DNA.

> 
> - How much arm-twisting would need to be done to use
> protein sequences
>   as the base display ?

None.

> 
> - Is there another technology/program better suited
> to do these displays ?

The main issue with, say, putting up a swiss-prot DAS
server is that DAS would tend to publish every
sequence ID. For genomes this is not a problem (one
per chromosome, or perhaps each large bit of
assembly). For swiss-prot, you will flood clients with
IDs. On the other hand, if you don't publish these IDs
as top-level entry points, there is no DAS way to
discover what IDs are present in a server. Of course,
if you want to provide annotation for a small number
of proteins (say less than a 1000) then this is not a
problem.

So - is there an official plan for dealing with
proteins?

Matthew

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