Contextual PSI-BLAST Project

CTX-PSI-BLAST is an extension of NCBI Toolkit that incorporates contextual alignment model [3,4] into the iterative version of BLAST algorithm known as PSI-BLAST [1]. It allows 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.

How to compile the source code?

The version of NCBI Toolkit used to implement contextual extension was Mar_17_2008. It is available at the NCBI FTP site. The source code was compiled under Linux PLD with GCC 4.4.1 and it is suggested to use GCC in version 4.4.1 at least. The list of all modified files can be found in the readme.txt file contained in the distribution.
To build an application run the following in the project root directory:

$ ./configure --without-debug; cd GCC{version}-Release/build; make all_r

CTX-PSI-BLAST executable file (psiblast) can be found in GCC{version}-Release/bin.

How to use the program?

The following command runs the standard version of PSI-BLAST:

$ ./psiblast -in query -db database -num_iteration iter -out output_file

where

query is the query sequence in FASTA format;
database is the name of database to scan for significant alignments;
iter is the number of iterations to be run; PSI-BLAST may run less number of iterations then specified if a search converges;
output_file is a file to which the program output will be written; if a specified file exists, it will be overwritten.

The contextual version of PSI-BLAST requires two additional parameters:

ctx_matrix defines the contextual substitution table, e.g. the CTX-BLOSUM62, the contextual counterpart of BLOSUM62
ctx_stat defines the file containing the parameters for statistical significance calculation in the following order: alpha, beta, lambda and K. Parameters must be separated with a single space.

The exemplary usage of CTX-PSI-BLAST on the NR database performing 6 iterations is the following:

$ ./psiblast -in 1ceo.seq -db nr -num_iteration 6 -out 1ceo.out -ctx_matrix blosum62.nrm -ctx_stat stat.txt

References

[1] S.F. Altschul, T.L. Madden, A.A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D.J. Lipman. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research, 25:3389-3402, 1997.
[2] I. Friedberg, T. Kaplan, and H. Margalit. Evaluation of PSI-BLAST alignment accuracy in comparison to structural alignments. Protein Science, Cambridge University Press, 9:2278-2284, 2000.
[3] A. Gambin and J. Tyszkiewicz. Substitution matrices for contextual alignment. Journees Ouvertes Biologie Informatique Mathematique, J. Nicolas and C. Thermes (eds.), 227-238, 2002.
[4] A. Gambin, S. Lasota, R. Szklarczyk, J. Tiuryn, and J. Tyszkiewicz. Contextual Alignment of Biological Sequences. Proc. ECCB 02, Bioinformatics, Oxford University Press, 18:116-127, 2002.

Contextual PSI-BLAST Project

How to compile the source code?

How to use the program?

References

Downloads

Contact