Identifying repeat domains in large genomes

Genome Biology
Degui ZhiPavel A Pevzner

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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Citations

Jul 18, 2006·Nucleic Acids Research·Neil C JonesBenjamin J Raphael
Feb 22, 2008·Nucleic Acids Research·Surya SahaDaniel G Peterson
Oct 24, 2008·Nucleic Acids Research·Cristian TaccioliCarlo Maria Croce
Dec 18, 2007·Genome Research·Mark J Chaisson, Pavel A Pevzner
Dec 5, 2006·BMC Genomics·Ralph T WiedmannJohn W Keele
Apr 22, 2008·Source Code for Biology and Medicine·Nicolas J Parker, Andrew G Parker
Feb 20, 2015·PLoS Genetics·Alexsandra SchneiderEduardo Eizirik
Jun 17, 2016·Bioinformatics·Carly E SchaefferJohn E Karro
Aug 19, 2016·Proceedings of the National Academy of Sciences of the United States of America·Jianwei ZhangQifa Zhang
Sep 8, 2021·Nature Cell Biology·Hongdao ZhangJianmin Li
Jul 20, 2007·Chemical Reviews·Haixu Tang

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Methods Mentioned

BETA
AAGTS

Software Mentioned

BLASTN
Repbase Update
ABA
RepeatMasker
Perl scripts
BLAT
RECON
RepeatFinder
CLUSTALW
RepeatGluer

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