CTX-BLAST: context sensitive version of protein BLAST.
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.


BACKGROUND
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.


BACKGROUND
Supplementary data are available at Bioinformatics online.
Gambin
Anna
A
Institute of Informatics, Warsaw University, Banacha 2, 02-097, Warsaw, Poland. aniag@mimuw.edu.pl
Wojtalewicz
Piotr
P
D000465:Algorithms; D000595:Amino Acid Sequence; D003198:Computer Simulation; D008956:Models, Chemical; D015233:Models, Statistical; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry*; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
D011506:Proteins