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Bioinformatics 2005 21(Suppl 1):i351-i358; doi:10.1093/bioinformatics/bti1018
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

De novo identification of repeat families in large genomes

Alkes L. Price , Neil C. Jones and Pavel A. Pevzner *

Department of Computer Science and Engineering, University of California San Diego La Jolla, CA 92093-0114, USA

*To whom correspondence should be addressed.

Every time we compare two species that are closer to each other than either is to humans, we get nearly killed by unmasked repeats.

Webb Miller (Personal communication)

Motivation: De novo repeat family identification is a challenging algorithmic problem of great practical importance. As the number of genome sequencing projects increases, there is a pressing need to identify the repeat families present in large, newly sequenced genomes. We develop a new method for de novo identification of repeat families via extension of consensus seeds; our method enables a rigorous definition of repeat boundaries, a key issue in repeat analysis.

Results: Our RepeatScout algorithm is more sensitive and is orders of magnitude faster than RECON, the dominant tool for de novo repeat family identification in newly sequenced genomes. Using RepeatScout, we estimate that ~2% of the human genome and 4% of mouse and rat genomes consist of previously unannotated repetitive sequence.

Availability: Source code is available for download at http://www-cse.ucsd.edu/groups/bioinformatics/software.html

Contact: ppevzner{at}cs.ucsd.edu

Received on January 15, 2005; accepted on March 27, 2005

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