Identifying repeat domains in large genomes

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 recover...

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Detalles Bibliográficos
Autores principales: Zhi, Degui, Raphael, Benjamin J, Price, Alkes L, Tang, Haixu, Pevzner, Pavel A
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2006
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1431705/
https://www.ncbi.nlm.nih.gov/pubmed/16507140
http://dx.doi.org/10.1186/gb-2006-7-1-r7
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author Zhi, Degui
Raphael, Benjamin J
Price, Alkes L
Tang, Haixu
Pevzner, Pavel A
author_facet Zhi, Degui
Raphael, Benjamin J
Price, Alkes L
Tang, Haixu
Pevzner, Pavel A
author_sort Zhi, Degui
collection PubMed
description 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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spelling pubmed-14317052006-04-07 Identifying repeat domains in large genomes Zhi, Degui Raphael, Benjamin J Price, Alkes L Tang, Haixu Pevzner, Pavel A Genome Biol Method 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. BioMed Central 2006 2006-01-31 /pmc/articles/PMC1431705/ /pubmed/16507140 http://dx.doi.org/10.1186/gb-2006-7-1-r7 Text en Copyright ©2006 Zhi et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Method
Zhi, Degui
Raphael, Benjamin J
Price, Alkes L
Tang, Haixu
Pevzner, Pavel A
Identifying repeat domains in large genomes
title Identifying repeat domains in large genomes
title_full Identifying repeat domains in large genomes
title_fullStr Identifying repeat domains in large genomes
title_full_unstemmed Identifying repeat domains in large genomes
title_short Identifying repeat domains in large genomes
title_sort identifying repeat domains in large genomes
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1431705/
https://www.ncbi.nlm.nih.gov/pubmed/16507140
http://dx.doi.org/10.1186/gb-2006-7-1-r7
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