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Genome Biol. 2006;7(1):R7. Epub 2006 Jan 31.

Identifying repeat domains in large genomes.

Zhi D, Raphael BJ, Price AL, Tang H, Pevzner PA.

Source

Bioinformatics Program, University of California, San Diego, CA 92093-0419, USA. dzhi@ucsd.edu

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.

PMID:: 16507140; [PubMed - indexed for MEDLINE]
PMCID: PMC1431705

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