REMiner-II: A tool for rapid identification and configuration of repetitive element arrays from large mammalian chromosomes as a single query

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Genes occupy similar to 3% of the human and mouse genomes whereas repetitive elements (REs), whose biologic functions are largely uncharacterized, constitute greater than 50%. A heterogeneous population of RE arrays (arrangement structures) is formed by combinations of various REs in mammalian genomes. In this study. REMiner-II was refined from the original REMiner for a more efficient identification and configuration of RE arrays from large queries (e.g., human chromosomes) using an unbiased self-alignment protocol. Chromosome-wide RE array profiles for the entire sets of human and mouse chromosomes were obtained using REMiner-II on a personal computer. REMiner-II provides 10 adjustable parameters and three data output modes to accommodate different experimental settings and/or goals. Examination of the human and mouse chromosome data using the REMiner-II viewer revealed species-specific libraries of complexly organized RE arrays. In conclusion, REMiner-II is an efficient tool for chromosome-wide identification and characterization of RE arrays from mammalian genomes. (C) 2012 Elsevier Inc. All rights reserved.
Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
Issue Date
2012-09
Language
English
Article Type
Article
Keywords

DNA-SEQUENCES; LTR RETROTRANSPOSONS; HUMAN GENOME; REPEATS; SEARCH; GENERATION; EFFICIENT; PROTEIN; FINDER; BLAST

Citation

GENOMICS, v.100, no.3, pp.131 - 140

ISSN
0888-7543
DOI
10.1016/j.ygeno.2012.06.006
URI
http://hdl.handle.net/10203/104030
Appears in Collection
EE-Journal Papers(저널논문)
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