Home > Archives > Additional Archives > Nickolay Kolchanov   Nickolay Kolchanov Institute of Cytology and Genetics Siberian Branch of the Russian Academy of Sciences Novosibirsk, Russia http://wwwmgs.bionet.nsc.ru/programs/CRASP/   Abstract: The software package CRASP is designed to detect the pairs of positions whereat the substitutions are fixed in a coadaptive mode; clusters of such positions (or coadaptive networks); and integral physico-chemical characteristics of the proteins that are conserved mainly due to coadaptive substitutions of their amino acid residues. CRASP has a HTML interface and is installed with the server of the Laboratory of theoretical genetics at http://wwwmgs.bionet.nsc.ru/programs/CRASP/. Multiple alignment of the sequences of a protein family is used as an input data. Three major problems arise while analyzing coadaptive substitutions: (1) Taking into account evolutionary dependence of the sequences analyzed; (2) Taking into account indirect (mediated) correlations; and (3) The problem of stability of correlation coefficient estimates. The ways to solve these problems in the CRASP package are discussed. The approach developed was applied to analysis of protein families of DNA binding domains of transcription factors as well as families of protein sequences obtained experimentally by artificial selection technique. The analysis carried out demonstrates that fixation of coadaptive substitutions is a common feature of protein families evolution.
	Home | SDSC | UCSD | Campus Map | Contact Info
	The San Diego Supercomputer Center (SDSC) is a research unit of the University of California, San Diego, and the leading-edge site of the National Partnership for Advanced Computational Infrastructure. SDSC researchers conduct studies in computational science, develop high-performance computing and networking technologies, and participate in NPACI activities. SDSC -- UC San Diego, MC 0505 -- 9500 Gilman Drive -- La Jolla, CA 92093-0505 -- 858-534-5000 -- 858-534-5152 (fax) info@sdsc.edu © 2001, The Regents of the University of California