title: REViewer: a tool for linear visualization of repetitive elements within a sequence query.
abstract: A species-specific population of arrangements of repetitive elements (REs), called RE arrays, exists in the human and mouse genomes. We developed an RE analytical tool, named REViewer, for visualizing RE occurrences within RE arrays and other genomic regions as an interactive line map. REViewer utilizes an RE reference library which is established with two RE types: 1) REMiner-generated undefined REs and 2) RepeatMasker-derived defined REs. RE occurrences within queries are visualized as a line map using these two RE types. The REViewer's controller provides analytical options, such as zoom, customization of axis unit, and RE type selection. The functionality of REViewer was evaluated using the human chromosome Y sequence. The REViewer is determined to be an efficient tool that facilitates visualization of up to 6000 REs in RE arrays and other genomic regions. The maximum query size is linked to the RE mining tools (e.g., REMiner, RepeatMasker), not to REViewer.
authors.affiliation: Department of Electrical Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, South Korea.
authors.forename: Ri-Na
authors.initials: RN
authors.lastname: You
authors.forename: Woo-Chan
authors.initials: WC
authors.lastname: Kim
authors.forename: Kang-Hoon
authors.initials: KH
authors.lastname: Lee
authors.forename: Young-Kwan
authors.initials: YK
authors.lastname: Lee
authors.forename: Kyung-Seop
authors.initials: KS
authors.lastname: Shin
authors.forename: Kiho
authors.initials: K
authors.lastname: Cho
authors.forename: Dong-Ho
authors.initials: DH
authors.lastname: Cho
mesh_terms: D000818:Animals; D041322:Chromosomes, Human, Y / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining; D030541:Databases, Genetic; D016678:Genome; D015894:Genome, Human; D006801:Humans; D051379:Mice; D012091:Repetitive Sequences, Nucleic Acid; D016415:Sequence Alignment; D017421:Sequence Analysis / Q000379:methods*; D012984:Software; D013045:Species Specificity
keywords: Linear visualization; RE array; REMiner; RepeatMasker; Repetitive element; Repetitive element array
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