Contextual BLAST Project.
We present a software tool called CTX-BLAST that incorporates contextual alignment model into the popular protein BLAST program. Our efficient alignment tool allows us to investigate the effect of context-dependency in the protein alignment in genomic scale. 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.
The following command runs the standard version of BLAST:
where program is in our case blastp (i.e. protein version of BLAST tool),
database is the name of database to scan for significant alignments,
query is the query sequence in FASTA format.
The contextual version of BLAST requires two additional parameters:
C defines the contextual substitution table, e.g. the CTX-BLOSUM62, the contextual counterpart of BLOSUM62
x defines the file containing the parameters for statistical significance calculation in the following order: alpha, beta, lambda and K.
The exemplary usage of CTX-BLAST on the COG database "kyva" is the following:
Here is the example invocation:
All programs you can download here.
dinero47 at gmail.com
pw201111 at students.mimuw.edu.pl