Question: Aligning Two Proteins With Their Domains/Annotations
7
gravatar for Pierre Lindenbaum
9.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum127k wrote:

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

annotation alignment protein • 2.3k views
ADD COMMENTlink modified 9.0 years ago by Michael Schubert6.9k • written 9.4 years ago by Pierre Lindenbaum127k
2

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

ADD REPLYlink modified 6 months ago by RamRS26k • written 9.1 years ago by Pierre Lindenbaum127k
9
gravatar for Alastair Kerr
9.4 years ago by
Alastair Kerr5.2k
Manchester/UK/Cancer Biomarker Centre at CRUK-MI
Alastair Kerr5.2k wrote:

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.

ADD COMMENTlink modified 9.4 years ago • written 9.4 years ago by Alastair Kerr5.2k
5
gravatar for Darked89
9.4 years ago by
Darked894.2k
Barcelona, Spain
Darked894.2k wrote:

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

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

ADD COMMENTlink written 9.4 years ago by Darked894.2k
3
gravatar for Pierre Lindenbaum
9.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum127k wrote:

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:

ADD COMMENTlink modified 7 months ago by RamRS26k • written 9.4 years ago by Pierre Lindenbaum127k
1
gravatar for Michael Schubert
9.1 years ago by
Cambridge, UK
Michael Schubert6.9k wrote:

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.

ADD COMMENTlink written 9.1 years ago by Michael Schubert6.9k
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