Cascade PSI-BLAST is a search method that detects distant similarities in proteins through the rigorous propagation of PSI-BLAST. In this approach, we perform a 'first generation' PSI-BLAST search for a query in a user-selected database. This could be PFAM, SWISSPROT or SCOP. Hits detected at the end of the first generation serve as seeds with which a 'second generation' of PSI-BLAST can be initiated. The choice of seeds sequences is left to the user. New hits identified at the end of the second generation are used to propagate further generations of the search. Such a non-directed search process that allows each hit to scan protein sequence space in a non-directed manner can detect distant similarities in proteins that may not be seen through traditional use of search methods such as PSI-BLAST. In earlier assessments, this search method has detected ~35% more relationships at the level of superfamily and improved coverages in protein families by 15%.
To submit a job on this server click here (or Cascade PSI-BLAST form).
Project Led By:   N. Srinivasan, (email@example.com) R. Sowdhamini
Other Contributors:   S. Sandhya,  K. R. Abhinandan,  S. Chakrabarti,  Dinesh D.C.
Maintained by:   Swapnil S. Mahajan(firstname.lastname@example.org)
Sandhya S, Chakrabarti S, Abhinandan KR, Sowdhamini R, Srinivasan N:Assessment of a rigorous transitive profile based search method to detect remotely similar proteins. J Biomol Struct Dyn. 2005 Dec;23(3):283-98. Click here for PDF.