Aligning Two Proteins With Their Domains/Annotations

Question

[Pierre Lindenbaum]

Hi all,

I'd like to align two peptides 'A' & 'B':

• 'A' is an annotated entry from swissprot
• 'B' is a mutated form of 'A'

In the alignment, I'd like to see where are the domains/annotations from 'A' overlapping 'B'.

Something that would look like this:

            <===========> Zinc Finger
                                 <=========> TPR Domain
WILD: LAATHEFKQA CQLCYPKTGP RAGDYTYREG LEHKCKRDIL
    : |||||||||| ||| |||||| |||||||||| ||||||||||
MUT : LAATHEFKQA CQLGYPKTGP RAGDYTYREG LEHKCKRDIL

do you know if such tool exists ?

Thanks,

Pierre

[Pierre Lindenbaum]

This question was featured in http://www.slideshare.net/lindenb/notch2-backstage

Answer 1

[Alastair Kerr]

Jalview will be able to show this. You can read in the features from your own feature file (e.g. gff) or from your own DAS server.

Answer 2

[Darked89]

If your protein is in PDB or Uniprot you may try SPICE (also DAS based):

http://www.dasregistry.org/spice/index.shtml

Answer 3

[Pierre Lindenbaum]

I've answered to my own question through this post

My tools reads a BLAST/XML files, search for the annotations in Genbank and displays the alignments:

Answer 4

[Michael Schubert]

For reference and because I was/am facing a similar problem: jsDAS

jsDAS is a javascript client library for DAS. It offers web developers full access to the data contained in the DAS network from inside the browser. It takes care of the communication with the servers and the data parsing and offers a simple yet powerful API to access all the received data.