title: REMiner: a tool for unbiased mining and analysis of repetitive elements and their arrangement structures of large chromosomes.
abstract: 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.
authors.affiliation: Division of Electrical Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.
authors.forename: Byung-Ik
authors.initials: BI
authors.lastname: Chung
authors.forename: Kang-Hoon
authors.initials: KH
authors.lastname: Lee
authors.forename: Kyung-Seop
authors.initials: KS
authors.lastname: Shin
authors.forename: Woo-Chan
authors.initials: WC
authors.lastname: Kim
authors.forename: Deug-Nam
authors.initials: DN
authors.lastname: Kwon
authors.forename: Ri-Na
authors.initials: RN
authors.lastname: You
authors.forename: Young-Kwan
authors.initials: YK
authors.lastname: Lee
authors.forename: Kiho
authors.initials: K
authors.lastname: Cho
authors.forename: Dong-Ho
authors.initials: DH
authors.lastname: Cho
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D041322:Chromosomes, Human, Y / Q000235:genetics*; D019295:Computational Biology; D057225:Data Mining; D016678:Genome; D006801:Humans; D016247:Information Storage and Retrieval; D020407:Internet; D008969:Molecular Sequence Data; D012091:Repetitive Sequences, Nucleic Acid; D016415:Sequence Alignment; D014584:User-Computer Interface