The CRASP package was developed to analyze correlated residue substitutions in multiple sequence alignments of a protein family. We proceeded on the assumption that the functionally related pairs of amino acid residues might have evolved dependently and vice versa, the co-ordinated mutations at certain protein positions can reveal the functionally important interactions between the residues at these positions. In particular, some of the detected correlations are presumably compensatory because of the proximity of the residues at the correlated positions. To date, a range of methods for the detection and analysis of coordinated residue substitutions have been developed. With our approach, such correlations were analyzed in terms of the physicochemical property values. We believe that these characteristics reflect physical and chemical interactions between residues.

How to use:

To input the data, copy them to the clipboard and paste into the text input field. To do so, press the Ctrl-Ins or Ctrl-V key combination. Input the phylogenetic tree in PHYLIP format in the "Phylogenetic tree input area (PHYLIP format)" if you will use phylogenetic tree weighting scheme. Select physicochemical property and weighting schemes from corresponding menus. After loading the data into fields and parameter setting, to launch the program, press the "Submit" button with the mouse. The server will accept a file as a computational task. To launch the control example, move to the "Example" link.

The results window appear at the right panel after the program is completed. This page contains links for displaying the calculated results. For the general results overview, press the "General results" link. For the plot of correlation matrix, press the "Pair correlation plot " link. To view clustering diagram of correlated positions, the user presses the "Clusters of correlated positions" link. To view statistics of physico-chemical properties in alignment columns, the user presses "Positional data" link. To view statistics of amino acids in alignment columns, the user presses " AminoAcid occurences at alignment positions" link. To view the distribution of correlation coefficients, press "Matrix elements distribution" link. Clicking the " Significantly correlating pairs" bring up a new browser window with list of position pairs with significantly correlating positions. Pressing to the "Return to the program" link will return the user can go back to the start page.

Multiple protein sequence alignment in FASTA format, phylogenetic tree in PHYLIP format

Correlation coefficients matrix