title: Identifying repeat domains in large genomes.
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.
authors.affiliation: Bioinformatics Program, University of California, San Diego, CA 92093-0419, USA. dzhi@ucsd.edu
authors.forename: Degui
authors.initials: D
authors.lastname: Zhi
authors.forename: Benjamin J
authors.initials: BJ
authors.lastname: Raphael
authors.forename: Alkes L
authors.initials: AL
authors.lastname: Price
authors.forename: Haixu
authors.initials: H
authors.lastname: Tang
authors.forename: Pavel A
authors.initials: PA
authors.lastname: Pevzner
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D015723:Gene Library; D016678:Genome / Q000235:genetics*; D023281:Genomics; D006801:Humans; D008969:Molecular Sequence Data; D010802:Phylogeny; D012091:Repetitive Sequences, Nucleic Acid / Q000235:genetics*