Identifying repeat domains in large genomes.

TitleIdentifying repeat domains in large genomes.
Publication TypeJournal Article
Year of Publication2006
AuthorsZhi D, Raphael BJ, Price AL, Tang H, Pevzner PA
JournalGenome Biol
Volume7
Issue1
PaginationR7
Date Published2006
ISSN1465-6914
KeywordsAlgorithms, Animals, Base Sequence, Caenorhabditis elegans, Databases, Nucleic Acid, Evolution, Molecular, Gene Library, Genome, Genomics, Humans, Molecular Sequence Data, Phylogeny, Repetitive Sequences, Nucleic Acid
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.

DOI10.1186/gb-2006-7-1-r7
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/16507140?dopt=Abstract
PMCPMC1431705
Alternate TitleGenome Biol.
PubMed ID16507140