Question: How To Predict Conserved Phosphorylation Sites From Multiple Alignment
7
gravatar for Michael Kuhn
10.0 years ago by
Michael Kuhn5.0k
EMBL Heidelberg
Michael Kuhn5.0k wrote:

Is there a tool that looks for phosphorylation sites in multiple aligned sequences and scores them by conservation (e.g. by combining the normal scores for the same site in multiple species)?

prediction multiple • 4.5k views
ADD COMMENTlink written 10.0 years ago by Michael Kuhn5.0k
5
gravatar for Fred Fleche
10.0 years ago by
Fred Fleche4.3k
Paris, France
Fred Fleche4.3k wrote:
ADD COMMENTlink modified 12 months ago by RamRS30k • written 10.0 years ago by Fred Fleche4.3k
4
gravatar for Neilfws
10.0 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

There are at least a dozen online tools that predict phosphorylation sites, using a variety of methods. Most of them simply scan a single input sequence for known motifs of specific kinase families, built using some fairly standard method (e.g. HMMs).

Surprisingly, there does not seem to be a tool to look for conserved sites in multiple sequences. However, people have used this approach: see for example Comparative Analysis Reveals Conserved Protein Phosphorylation Networks Implicated in Multiple Diseases.

I guess it would not be too difficult to build such a tool, using the alignment module of your favourite Bio* project to extract and score the appropriate columns from an alignment.

ADD COMMENTlink written 10.0 years ago by Neilfws48k
3
gravatar for Niallhaslam
9.8 years ago by
Niallhaslam2.3k
Dublin
Niallhaslam2.3k wrote:

If you are interested in the conservation then take a look at Claudia Chica's server (http://conscore.embl.de/html/index.html). It is designed to give a score for protein motifs.

More information is available in the phospho.ELM server paper which has the reference to the actual implementation and some information on the usage of the conservation score in phospho.ELM.

Manuscript: http://nar.oxfordjournals.org/content/early/2010/11/08/nar.gkq1104.abstract

Webservice here: conscore.embl.de/CS.wsdl

ADD COMMENTlink written 9.8 years ago by Niallhaslam2.3k

Very interesting! What is the required format for the multiple sequence alignment? I tried FASTA, but I got an error: "Query sequence (or query sequence name) not present in the alignment." (specifying 9606.ENSP00000255289 from this alignment: http://pastebin.com/Y6F7m2H6 )

ADD REPLYlink written 9.8 years ago by Michael Kuhn5.0k
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