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Bioinformatics Advance Access published online on July 15, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth408
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received April 16, 2004
Revised July 5, 2004
Accepted July 7, 2004

Article

Reducing storage requirements for biological sequence comparison

Michael Roberts 1, Wayne Hayes 1, Brian R. Hunt 1, Stephen M. Mount 1, James A. Yorke 1*

1 Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742-2431

* To whom correspondence should be addressed. E-mail: yorke{at}ipst.umd.edu.


  Abstract

Motivation: Comparison of nucleic acid and protein sequences is a fundamental tool of modern bioinformatics. A dominant method of such string matching is the "seed-and-extend" approach, in which occurrences of short subsequences called "seeds" are used to search for potentially longer matches in a large database of sequences. Each such potential match is then checked to see if it extends beyond the seed. To be effective, the seed-and-extend approach needs to catalogue seeds from virtually every substring in the database of search strings. Projects such as mammalian genome assemblies and large-scale protein matching, however, have such large sequence databases that the resulting list of seeds cannot be stored in RAM on a single computer. This significantly slows the matching process.

Results: We present a simple and elegant method in which only a small fraction of seeds, called "minimizers", needs to be stored. Using minimizers can speed up string-matching computations by a large factor while missing only a small fraction of the matches found using all seeds.


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