title: REMiner-II: a tool for rapid identification and configuration of repetitive element arrays from large mammalian chromosomes as a single query.
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.
authors: Department of Electrical Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.
authors: Woo-Chan
authors: WC
authors: Kim
authors: Kang-Hoon
authors: KH
authors: Lee
authors: Kyung-Seop
authors: KS
authors: Shin
authors: Ri-Na
authors: RN
authors: You
authors: Young-Kwan
authors: YK
authors: Lee
authors: Kiho
authors: K
authors: Cho
authors: Dong-Ho
authors: DH
authors: Cho
mesh_terms: D000465:Algorithms; D000818:Animals; D002875:Chromosomes / Q000235:genetics*; D019295:Computational Biology / Q000379:methods; D057225:Data Mining / Q000379:methods*; D030541:Databases, Genetic; D015894:Genome, Human; D006801:Humans; D020407:Internet; D008322:Mammals / Q000235:genetics*; D051379:Mice; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D012091:Repetitive Sequences, Nucleic Acid; D016415:Sequence Alignment / Q000379:methods; D012984:Software; D013045:Species Specificity; D013997:Time Factors