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Bioinformatics Advance Access published online on October 27, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti076
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received July 13, 2004
Revised September 23, 2004
Accepted September 24, 2004

Article

Fast and accurate database homology search using upper bounds of local alignment

Masumi Itoh 1*, Susumu Goto 1, Tatsuya Akutsu 1, and Minoru Kanehisa 1

1 Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan

* To whom correspondence should be addressed.
Masumi Itoh, E-mail: itoh{at}kuicr.kyoto-u.ac.jp


  Abstract

Motivation: It is widely recognized that homology search and ortholog clustering are very useful for analyzing biological sequences. However, recent growth of sequence database size makes homolog detection difficult, and rapid and accurate methods are required.

Results: We present a novel method for fast and accurate homology detection, assuming that the Smith-Waterman scores between all similar sequence pairs in a target database are computed and stored. In this method, SW-alignment is computed only if the upper bound, which is derived from our novel inequality, is higher than the given threshold. In contrast to other methods such as FASTA and BLAST, this method is guaranteed to find all sequences whose scores against the query are higher than the specified threshold. The results of computational experiments suggest that the method is dozens of times faster than SSEARCH if genome sequence data of closely related species are available.

Availability: The programs for fast homolog detection can be downloaded from ftp://ftp.kuicr.kyoto-u.ac.jp/itoh/.


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