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Identifying repeat domains in large genomes

Degui Zhi1*, Benjamin J Raphael2, Alkes L Price3, Haixu Tang4 and Pavel A Pevzner2

Author Affiliations

1 Bioinformatics Program, University of California, San Diego, CA 92093-0419, USA

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

3 Department of Genetics, Harvard Medical School, Boston, MA 02115, USA

4 School of Informatics and Center for Genomics and Bioinformatics, Indiana University, Bloomington, IN 47408, USA

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Genome Biology 2006, 7:R7  doi:10.1186/gb-2006-7-1-r7

Published: 31 January 2006

Abstract

We present a graph-based method for the analysis of repeat families in a repeat library. We build a repeat domain graph that decomposes a repeat library into repeat domains, short subsequences shared by multiple repeat families, and reveals the mosaic structure of repeat families. Our method recovers documented mosaic repeat structures and suggests additional putative ones. Our method is useful for elucidating the evolutionary history of repeats and annotating de novo generated repeat libraries.