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Aligning Two Proteins With Their Domains/Annotations

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

alignment annotation protein
• 4,679 views • link
updated by Michael Schubert Michael Schubert • written by Pierre Lindenbaum Pierre Lindenbaum

4 answers

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.

• 0 views • link
written by Alastair Kerr Alastair Kerr

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

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

• 1 views • link
written by Darked89 Darked89

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:

• 0 views • link
updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

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.

• 0 views • link
written by Michael Schubert Michael Schubert

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