[DAS] Displaying protein sequences and features

Tony Cox avc at sanger.ac.uk
Tue Apr 22 17:28:42 EDT 2003

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

....and several simple-minded fools who would like to help :)

+>In principle, it is not very tied to DNA.

in practive there are some problems since a lot of the underlying code is tied
to DNA rather than protein sequences. Foe example, dazzle falls over getting the
sequence length when serving proteins.

+>> - How much arm-twisting would need to be done to use
+>> protein sequences
+>>   as the base display ?
+>> - 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
+>So - is there an official plan for dealing with

Not that I know of. I guess the spec needs to be remoulded to make it more
inclusive and handle proetin sequence properly. The entry points problem is
always going to be hard to deal with. If somebody does and entry_points request
on our PDAS server and doesn't cache the results then they are in for a long


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Tony Cox			Email:avc at sanger.ac.uk
Sanger Institute		WWW:www.sanger.ac.uk
Wellcome Trust Genome Campus	Webmaster
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