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Nucleic Acids Research 2005 33(14):4563-4577; doi:10.1093/nar/gki767
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Published online 12 August 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

Using multiple alignments to improve seeded local alignment algorithms

Jason Flannick* and Serafim Batzoglou

Department of Computer Science, Stanford University Stanford, CA 94304, USA

*To whom correspondence should be addressed. Tel: +1 650 289 0295; Fax: +1 650 725 1449; Email: flannick{at}cs.stanford.edu

Received June 8, 2005. Revised July 6, 2005. Accepted July 27, 2005.

Multiple alignments among genomes are becoming increasingly prevalent. This trend motivates the development of tools for efficient homology search between a query sequence and a database of multiple alignments. In this paper, we present an algorithm that uses the information implicit in a multiple alignment to dynamically build an index that is weighted most heavily towards the promising regions of the multiple alignment. We have implemented Typhon, a local alignment tool that incorporates our indexing algorithm, which our test results show to be more sensitive than algorithms that index only a sequence. This suggests that when applied on a whole-genome scale, Typhon should provide improved homology searches in time comparable to existing algorithms.

Correspondence may also be addressed to Serafim Batzoglou. Tel: +1 650 723 3334; Fax +1 650 725 1449; Email: serafim{at}cs.stanford.edu


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