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Bioinformatics Advance Access published online on April 25, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm136
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

CTX-BLAST: context sensitive version of protein BLAST

Anna Gambin * and Piotr Wojtalewicz

Institute of Informatics, Warsaw University, Banacha 2, 02-097, Warsaw Poland

*To whom correspondence should be addressed. Dr. Anna Gambin, E-mail: aniag{at}mimuw.edu.pl


  Abstract

Summary: We present a software tool CTX-BLAST that incorporates contextual alignment model from (Gambin et al., 2002) into the popular protein BLAST program. Our alignment tool allows us to investigate the effect of context-dependency in the protein alignment much more efficient than using the dynamic algorithm of (Gambin et al., 2002). The software makes use of non-symmetric contextual substitution tables and calculates the statistical significance of a given alignment according to the contextual statistical model of (Gambin et al., 2006).

Results:

Availability: CTX-BLAST is an open source software freely available from www.sourceforge.net/projects/CTX-BLAST. A program for statistical estimation of E-value parameters and the contextual substitution table CTX-BLOSUM62 are also provided.

Associate Editor: Prof. Dmitrij Frishman

Received on November 27, 2006; revised on March 13, 2007; accepted on April 3, 2007

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