Identifying repeat domains in large genomes

Degui Zhi, Benjamin J. Raphael, Alkes L. Price, Haixu Tang, Pavel A. Pevzner

Research output: Contribution to journalArticle

19 Scopus citations

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.

Original languageEnglish (US)
Article numberR7
JournalGenome biology
Volume7
Issue number1
DOIs
StatePublished - Jan 31 2006
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Ecology, Evolution, Behavior and Systematics
  • Genetics
  • Cell Biology

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  • Cite this

    Zhi, D., Raphael, B. J., Price, A. L., Tang, H., & Pevzner, P. A. (2006). Identifying repeat domains in large genomes. Genome biology, 7(1), [R7]. https://doi.org/10.1186/gb-2006-7-1-r7