CTX-BLAST: context sensitive version of protein BLAST.

UNLABELLED: 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. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.