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Bioinformatics Advance Access published online on October 6, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm489
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© 2007 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

BiasViz: Visualization of amino acid biased regions in protein alignments

Matthew R. Huska 1,*, Henrik Buschmann 2 and Miguel A. Andrade-Navarro 1,3

1Molecular Medicine, Ottawa Health Research Institute, 501 Smyth Rd, Ottawa., ON, Canada K1H 8L6
2Department of Cell and Developmental Biology, John Innes Centre, Norwich UK
3Cellular and Molecular Medicine, Faculty of Medicine, University of Ottawa

*To whom correspondence should be addressed. Matthew R. Huska, E-mail: matthuska{at}alumni.uwaterloo.ca


  Abstract

Summary: About a third of all protein sequences have at least one composition biased region (CBR). Such regions might act as linkers between protein domains but often confer specific binding to various molecules; therefore their characterization in terms of their boundaries and over-represented residues is important. Analysis of CBRs in a particular sequence can be time consuming if several types of biases have to be explored and their position visualized. Assessment of the significance of the detected CBRs can be approached by comparison to homologous protein sequences. To assist this procedure, we have developed BiasViz, a tool that allows to graphically studying local amino acid composition in protein sequences of a multiple sequence alignment.

Availability: BiasViz java applet and source code can be accessed from http://biasviz.sourceforge.net.

Contact: matthuska{at}alumni.uwaterloo.ca.

Associate Editor: Dr. Limsoon Wong

Received on July 25, 2007; revised on July 25, 2007; accepted on September 14, 2007

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