Journal Article

Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains

R. Bhadra, S. Sandhya, K. R. Abhinandan, S. Chakrabarti, R. Sowdhamini and N. Srinivasan

in Nucleic Acids Research

Volume 34, issue suppl_2, pages W143-W146
Published in print July 2006 | ISSN: 0305-1048
Published online July 2006 | e-ISSN: 1362-4962 | DOI: http://dx.doi.org/10.1093/nar/gkl157

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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.

Journal Article.  1912 words.  Illustrated.

Subjects: Chemistry ; Biochemistry ; Bioinformatics and Computational Biology ; Genetics and Genomics ; Molecular and Cell Biology

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