[DAS] Displaying protein sequences and features

[Tony Cox]

On Tue, 22 Apr 2003, Kris Boulez wrote:

Funny you should ask this... I just set up a protein DAS server at Ensembl so
that we can use DAS to layer anotations on our protein displays.

I dragged the whole of Interpro into an LDAS schema. Not all domains have been
included. Domains without start/ed info or where status != "True" or "N" have
been excluded.

There are:

    730255 reference swissprot sequences
   3343535 domain annotations

It's a bit rough but it seems to run OK although I can't be sure that all of
the DAS commands will work properly since it is rather DNA-centric by design and
there is no assembly as such, so only the "features" request is probably of any
interest.

You can get to it from:

http://servlet.sanger.ac.uk:7070/perl/das/ens_pdas_ipro/

eg:

http://servlet.sanger.ac.uk:7070/perl/das/ens_pdas_ipro/features?segment=BMAL_HUMAN

gives:

<DASGFF>
<GFF version="1.01"
href="http://ecs3:7070/cgi-bin/das/ens_pdas_ipro/features?segment=BMAL_HUMAN">
<SEGMENT id="BMAL_HUMAN" start="1" stop="583" version="1.0">
   <FEATURE id="BMAL_HUMAN" label="BMAL_HUMAN">
      <TYPE id="Component:Protein"
category="structural">Component:Protein</TYPE>
      <METHOD id="Component">Component</METHOD>
      <START>1</START>
      <END>583</END>
      <SCORE>0</SCORE>
      <ORIENTATION>+</ORIENTATION>
      <PHASE>0</PHASE>
      <GROUP id="BMAL_HUMAN" />
   </FEATURE>
...
   <FEATURE id="PF00010" label="PF00010">
      <TYPE id="PFAM:Basic helix-loop-helix dimeriz"
category="miscellaneous">PFAM:Basic helix-loop-helix dimeriz</TYPE>
      <METHOD id="PFAM">PFAM</METHOD>
      <START>30</START>
      <END>83</END>
      <SCORE>0</SCORE>
      <ORIENTATION>+</ORIENTATION>
      <PHASE>0</PHASE>
      <GROUP id="PF00010" />
   </FEATURE>
</SEGMENT>
</GFF>
</DASGFF>


regards

Tony


+>[ I might make a complete fool of myself by asking the following, but
+>  anyway ]
+>
+>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 ?
+>
+>- 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 ?
+>
+>Kris,
+>--
+>Kris Boulez 				Tel: +32-9-241.11.00
+>AlgoNomics NV 				Fax: +32-9-241.11.02
+>Technologiepark 4 			email: kris.boulez at algonomics.com
+>B 9052 Zwijnaarde 			http://www.algonomics.com/
+>_______________________________________________
+>DAS mailing list
+>DAS at biodas.org
+>http://biodas.org/mailman/listinfo/das
+>

******************************************************
Tony Cox			Email:avc at sanger.ac.uk
Sanger Institute		WWW:www.sanger.ac.uk
Wellcome Trust Genome Campus	Webmaster
Hinxton				Tel: +44 1223 834244
Cambs. CB10 1SA			Fax: +44 1223 494919
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