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Bioinformatics Advance Access published online on May 14, 2008
Bioinformatics, doi:10.1093/bioinformatics/btn233
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© The Author (2008). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

ProBias: a web-server for the identification of user-specified types of compositionally biased segments in protein sequences.

Igor B. Kuznetsov

Gen*NY*sis Center for Excellence in Cancer Genomics, Department of Epidemiology and Biostatistics, One Discovery Drive, University at Albany, Rensselaer, NY 12144, USA

To whom correspondence should be addressed. Prof. Igor B. Kuznetsov, E-mail: IKuznetsov{at}albany.edu


  Abstract

Summary: Most proteins contain compositionally biased segments (CBS) in which one or more amino acid types are significantly over-represented. CBS that contain amino acids with similar chemical properties can have functional and structural importance. This paper describes ProBias, a web-server that searches a protein sequence for CBS composed of user-specified amino acid types. ProBias utilizes the discrete scan statistics to estimate statistical significance of CBS and is able to detect even subtle local deviations from the random independence model. The web-server also analyzes the global compositional bias of the input sequence. In the case of novel proteins that lack functional annotation, statistically significant CBS reported by ProBias can be used to guide the search for potential functionally important sites or domains.

Availability: Freely available at http://lcg.rit.albany.edu/ProBias

Contact: IKuznetsov{at}albany.edu

Associate Editor: Prof. John Quackenbush

Received on March 17, 2008; revised on May 11, 2008; accepted on May 12, 2008

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