CRASP: a program for analysis of coordinated substitutions in multiple alignments of protein sequences.

Recent results suggest that during evolution certain substitutions at protein sites may occur in a coordinated manner due to interactions between amino acid residues. Information on these coordinated substitutions may be useful for analysis of protein structure and function. CRASP is an Internet-available software tool for the detection and analysis of coordinated substitutions in multiple alignments of protein sequences. The approach is based on estimation of the correlation coefficient between the values of a physicochemical parameter at a pair of positions of sequence alignment. The program enables the user to detect and analyze pairwise relationships between amino acid substitutions at protein sequence positions, estimate the contribution of the coordinated substitutions to the evolutionary invariance or variability in integral protein physicochemical characteristics such as the net charge of protein residues and hydrophobic core volume. The CRASP program is available at http://wwwmgs.bionet.nsc.ru/mgs/programs/crasp/.