REMiner: A tool for unbiased mining and analysis of repetitive elements and their arrangement structures of large chromosomes

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Repetitive elements (REs) constitute a substantial portion of the genomes of human and other species; however, the RE profiles (type, density, and arrangement) within the individual genomes have not been fully characterized. In this study, we developed an RE analysis tool, called REMiner, for a chromosome-wide investigation into the occurrence of individual REs and arrangement of clusters of REs, and REMiner's functional features were examined using the human chromosome Y. The algorithm implemented by REMiner focused on unbiased mining of REs in large chromosomes and data interface within a viewer. The data from the chromosome demonstrated that REMiner is an efficient tool in regard to its capacity for a large query size and the availability of a high-resolution viewer, featuring instant retrieval of alignment data and control of magnification and identity ratio. The chromosome-wide survey identified a diverse population of ordered RE arrangements, which may participate in the genome biology. (C) 2011 Elsevier Inc. All rights reserved.
Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
Issue Date
2011-11
Language
English
Article Type
Article
Citation

GENOMICS, v.98, no.5, pp.381 - 389

ISSN
0888-7543
DOI
10.1016/j.ygeno.2011.07.002
URI
http://hdl.handle.net/10203/101140
Appears in Collection
EE-Journal Papers(저널논문)
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