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

Woo Chan Kim, Kang Hoon Lee, Kyung Seop Shin, Ri Na You, Young Kwan Lee, Kiho Cho, Dong Ho Cho

Research output: Contribution to journalArticle

8 Scopus citations

Abstract

Genes occupy ~. 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.

Original languageEnglish (US)
Pages (from-to)131-140
Number of pages10
JournalGenomics
Volume100
Issue number3
DOIs
StatePublished - Sep 2012

Keywords

  • Chromosome-wide
  • Mammalian genome
  • Mining
  • RE array
  • REMiner-II
  • Repetitive element

ASJC Scopus subject areas

  • Genetics

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