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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Authors: | Kim Woo-Chan Lee Kang-Hoon Shin Kyung-Seop You Ri-Na Lee Young-Kwan Cho Kiho Cho Dong-Ho |
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Institution: | Department of Electrical Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea. |
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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. |
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