REMiner: A tool for unbiased mining and analysis of repetitive elements and their arrangement structures of large chromosomes

Byung Ik Chung, Kang Hoon Lee, Kyung Seop Shin, Woo Chan Kim, Deug Nam Kwon, Ri Na You, Young Kwan Lee, Kiho Cho, Dong Ho Cho

Research output: Contribution to journalArticle

6 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)381-389
Number of pages9
JournalGenomics
Volume98
Issue number5
DOIs
StatePublished - Nov 2011

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Keywords

  • Chromosome-wide interactive mining
  • Genome
  • REMiner
  • Repetitive element
  • Repetitive element arrangement

ASJC Scopus subject areas

  • Genetics

Cite this

Chung, B. I., Lee, K. H., Shin, K. S., Kim, W. C., Kwon, D. N., You, R. N., Lee, Y. K., Cho, K., & Cho, D. H. (2011). REMiner: A tool for unbiased mining and analysis of repetitive elements and their arrangement structures of large chromosomes. Genomics, 98(5), 381-389. https://doi.org/10.1016/j.ygeno.2011.07.002