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Bioinformatics Advance Access published online on August 5, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth455
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received May 8, 2003
Revised July 26, 2004
Accepted July 27, 2004

Article

Highly-specific prediction of phosphorylation sites in proteins

Matthias Koenig 1* Niels Grabe 2

1 CeVis, University of Bremen, Universitaetsallee 29, 28359 Bremen, Germany
2 AgeLab Pharma GmbH, Grandweg 64, 22529 Hamburg, Germany

* To whom correspondence should be addressed. E-mail: koenig{at}cevis.uni-bremen.de.


  Abstract

Motivation: The prediction of short functional significant protein sequences has inherent problems. Predicting phosphorylation sites, problems come from the shortness of phosphorylation sites, the difficulties from maintaining many predefined different models of binding sites, the difficulties of obtaining highly sensitive predictions and of obtaining predictions with a constant sensitivity and specificity. The algorithm presented in this paper overcomes those problems.

Results: The proposed algorithm PHOSITE is based on case-based sequence analysis. This enables the prediction of phosphorylation sites with constant specificity and sensitivity. Furthermore, this method leads not only to the prediction of phosphorylation sites in general but also predicts the most probable type of kinase involved.

Availability: The tool PHOSITE implementing the presented method can be evaluated under the website http://www.phosite.com.


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