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Bioinformatics 2005 21(Suppl 1):i152-i158; doi:10.1093/bioinformatics/bti1003
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

PILER: identification and classification of genomic repeats

Robert C. Edgar 1,* and Eugene W. Myers 2

1 195 Roque Moraes Drive, Mill Valley, CA, USA
2Department of Computer Science, University of California Berkeley, CA, USA

*To whom correspondence should be addressed.

Summary: Repeated elements such as satellites and transposons are ubiquitous in eukaryotic genomes. De novo computational identification and classification of such elements is a challenging problem. Therefore, repeat annotation of sequenced genomes has historically largely relied on sequence similarity to hand-curated libraries of known repeat families. We present a new approach to de novo repeat annotation that exploits characteristic patterns of local alignments induced by certain classes of repeats. We describe PILER, a package of efficient search algorithms for identifying such patterns. Novel repeats found using PILER are reported for Homo sapiens, Arabidopsis thalania and Drosophila melanogaster.

Availability: The PILER software is freely available at http://www.drive5.com/piler

Contact: bob{at}drive5.com

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

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