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Bioinformatics Advance Access originally published online on January 28, 2009
Bioinformatics 2009 25(6):822-823; doi:10.1093/bioinformatics/btp054
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Fast computation of neighbor seeds

Lucian Ilie 1,* and Silvana Ilie 2

1Department of Computer Science, University of Western Ontario, London N6A 5B7 and 2Department of Mathematics, Ryerson University, Toronto, M5B 2K3, Ontario, Canada

*To whom correspondence should be addressed.


  Abstract

Motivation: Alignment of biological sequences is one of the most frequently performed computer tasks. The current state of the art involves the use of (multiple) spaced seeds for producing high quality alignments. A particular important class is that of neighbor seeds which combine high sensitivity with reduced space requirements. Current algorithms for computing good neighbor seeds are very slow (exponential).

Results: We give a polynomial-time heuristic algorithm that computes better neighbor seeds than previous ones while being several orders of magnitude faster.

Contact: ilie{at}csd.uwo.ca

Associate editor: John Quackenbush

Received on December 1, 2008; revised on January 7, 2009; accepted on January 22, 2009

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