Bioinformatics. 2007 Nov 15;23(22):3093-4. Epub 2007 Oct 6.

BiasViz: visualization of amino acid biased regions in protein alignments.

Huska MR, Buschmann H, Andrade-Navarro MA.

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Molecular Medicine, Ottawa Health Research Institute, 501 Smyth Road, Ottawa, ON, Canada. matthuska@alumni.uwaterloo.ca

Abstract

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.

PMID:: 17921493; [PubMed - indexed for MEDLINE]

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