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Bioinformatics Advance Access originally published online on April 25, 2007
Bioinformatics 2007 23(13):1686-1688; 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.


  Abstract

Summary: We present a software tool CTX-BLAST that incorporates contextual alignment model 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 previous dynamic algorithms. 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.

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.

Contact: aniag{at}mimuw.edu.pl

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Dmitrij Frishman

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

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