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Nucleic Acids Research Advance Access originally published online on May 8, 2009
Nucleic Acids Research 2009 37(Web Server issue):W53-W56; doi:10.1093/nar/gkp301
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W53-W56
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

SIB-BLAST: a web server for improved delineation of true and false positives in PSI-BLAST searches

Marianne M. Lee1, Michael K. Chan1,2,3,* and Ralf Bundschuh1,2,4,*

1The Ohio State Biophysics Program, 2Department of Biochemistry, 3Department of Chemistry and 4Department of Physics, Ohio State University, Columbus, OH 43210-1117, USA

*To whom correspondence should be addressed. Tel: +1 614 688 3978; Fax: +1 614 292 7557; Email: bundschuh{at}mps.ohio-state.edu Correspondence may also be addressed to Michael K. Chan. Tel: +1 614 292 8375; Fax: +1 614 292 6773; Email: chan{at}chemistry.ohio-state.edu.

Received January 28, 2009. Revised April 6, 2009. Accepted April 15, 2009.

A SIB-BLAST web server (http://sib-blast.osc.edu) has been established for investigators to use the SimpleIsBeautiful (SIB) algorithm for sequence-based homology detection. SIB was developed to overcome the model corruption frequently observed in the later iterations of PSI-BLAST searches. The algorithm compares resultant hits from the second iteration to the final iteration of a PSI-BLAST search, calculates the figure of merit for each ‘overlapped’ hit and re-ranks the hits according to their figure of merit. By validating hits generated from the last profile against hits from the first profile when the model is least corrupted, the true and false positives are better delineated, which in turn, improves the accuracy of iterative PSI-BLAST searches. Notably, this improvement to PSI-BLAST comes at minimal computational cost as SIB-BLAST utilizes existing results already produced in a PSI-BLAST search.


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