Identifying repeat domains in large genomes

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

doi:10.1186/gb-2006-7-1-r7

Identifying repeat domains in large genomes

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

Research output: Contribution to journal › Article › peer-review

25 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 language	English (US)
Article number	R7
Journal	Genome biology
Volume	7
Issue number	1
DOIs	https://doi.org/10.1186/gb-2006-7-1-r7
State	Published - Jan 31 2006
Externally published	Yes

All Science Journal Classification (ASJC) codes

Genetics
Ecology, Evolution, Behavior and Systematics
Cell Biology

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10.1186/gb-2006-7-1-r7

Cite this

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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.",

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AU - Raphael, Benjamin J.

AU - Price, Alkes L.

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AU - Pevzner, Pavel A.

PY - 2006/1/31

Y1 - 2006/1/31

N2 - 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.

AB - 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.

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Identifying repeat domains in large genomes

Abstract

All Science Journal Classification (ASJC) codes

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