Article |
Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains
1 Molecular Biophysics Unit, Indian Institute of Science 560 012, Bangalore, India 2 National Center for Biological Sciences, Tata Institute of Fundamental Research GKVK Campus, Bellary Road, Bangalore 560 065, India
*To whom correspondence should be addressed. Tel: +91 80 2293 2837; Fax: +91 80 2360 0535; Email: ns{at}mbu.iisc.ernet.in
Received February 3, 2006. Revised February 22, 2006. Accepted March 20, 2006.
Owing to high evolutionary divergence, it is not always possible to identify distantly related protein domains by sequence search techniques. Intermediate sequences possess sequence features of more than one protein and facilitate detection of remotely related proteins. We have demonstrated recently the employment of Cascade PSI-BLAST where we perform PSI-BLAST for many ‘generations’, initiating searches from new homologues as well. Such a rigorous propagation through generations of PSI-BLAST employs effectively the role of intermediates in detecting distant similarities between proteins. This approach has been tested on a large number of folds and its performance in detecting superfamily level relationships is 
35% better than simple PSI-BLAST searches. We present a web server for this search method that permits users to perform Cascade PSI-BLAST searches against the Pfam, SCOP and SwissProt databases. The URL for this server is http://crick.mbu.iisc.ernet.in/~CASCADE/CascadeBlast.html.
Present addresses: K. R. Abhinandan, Department of Biochemistry and Molecular Biology, University College, London, Gower Street, London WC1E 6BT, England
S. Chakrabarti, Computational Biology Branch, National Center for Biotechnology, Information (NCBI), National Library of Medicine (NLM), NIH, 8600, Rockville Pike, Bethesda, MD 20894, USA