Unbiased mining tool of repetitive elements and their arrangement structure for large size genomes

Woo Chan Kim; Kang Hoon Lee; Kyung Seop Shin; Ri Na You; Hyeon Seok Shin; Young Kwan Lee; Kiho Cho; Dong Ho Cho

doi:10.1109/ICTC.2010.5674772

Unbiased mining tool of repetitive elements and their arrangement structure for large size genomes

Woo Chan Kim, Kang Hoon Lee, Kyung Seop Shin, Ri Na You, Hyeon Seok Shin, Young Kwan Lee, Kiho Cho, Dong Ho Cho

Surgery

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

Genes are reported to constitute only 2-3% of the human genome, whereas repetitive elements (REs)make up a large portion of genomes of human and other eukaryotes. However, existing algorithms or tools for identification of REs as well as biological researches focus on the known specific REs. Thus, we design and implement a tool for unbiased mining of REs for large size genomes, called REMiner, in this paper. REMiner provides fast computation with low memory usage for the huge size of input genomic data. We show some interesting repeat patterns of the human chromosomes, which have not yet been reported. This chromosome-wide survey of complex, but highly-ordered RE array, will provide a foundation for a novel investigation into the genome.

Original language	English (US)
Title of host publication	2010 International Conference on Information and Communication Technology Convergence, ICTC 2010
Pages	513-514
Number of pages	2
DOIs	https://doi.org/10.1109/ICTC.2010.5674772
State	Published - 2010
Event	2010 International Conference on Information and Communication Technology Convergence, ICTC 2010 - Jeju, Korea, Republic of Duration: Nov 17 2010 → Nov 19 2010

Other

Other	2010 International Conference on Information and Communication Technology Convergence, ICTC 2010
Country	Korea, Republic of
City	Jeju
Period	11/17/10 → 11/19/10

ASJC Scopus subject areas

Computer Networks and Communications
Information Systems

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Kim, W. C., Lee, K. H., Shin, K. S., You, R. N., Shin, H. S., Lee, Y. K., Cho, K., & Cho, D. H. (2010). Unbiased mining tool of repetitive elements and their arrangement structure for large size genomes. In 2010 International Conference on Information and Communication Technology Convergence, ICTC 2010 (pp. 513-514). [5674772] https://doi.org/10.1109/ICTC.2010.5674772

Unbiased mining tool of repetitive elements and their arrangement structure for large size genomes. / Kim, Woo Chan; Lee, Kang Hoon; Shin, Kyung Seop; You, Ri Na; Shin, Hyeon Seok; Lee, Young Kwan; Cho, Kiho; Cho, Dong Ho.

2010 International Conference on Information and Communication Technology Convergence, ICTC 2010. 2010. p. 513-514 5674772.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Kim, WC, Lee, KH, Shin, KS, You, RN, Shin, HS, Lee, YK, Cho, K & Cho, DH 2010, Unbiased mining tool of repetitive elements and their arrangement structure for large size genomes. in 2010 International Conference on Information and Communication Technology Convergence, ICTC 2010., 5674772, pp. 513-514, 2010 International Conference on Information and Communication Technology Convergence, ICTC 2010, Jeju, Korea, Republic of, 11/17/10. https://doi.org/10.1109/ICTC.2010.5674772

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abstract = "Genes are reported to constitute only 2-3% of the human genome, whereas repetitive elements (REs)make up a large portion of genomes of human and other eukaryotes. However, existing algorithms or tools for identification of REs as well as biological researches focus on the known specific REs. Thus, we design and implement a tool for unbiased mining of REs for large size genomes, called REMiner, in this paper. REMiner provides fast computation with low memory usage for the huge size of input genomic data. We show some interesting repeat patterns of the human chromosomes, which have not yet been reported. This chromosome-wide survey of complex, but highly-ordered RE array, will provide a foundation for a novel investigation into the genome.",

author = "Kim, {Woo Chan} and Lee, {Kang Hoon} and Shin, {Kyung Seop} and You, {Ri Na} and Shin, {Hyeon Seok} and Lee, {Young Kwan} and Kiho Cho and Cho, {Dong Ho}",

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doi = "10.1109/ICTC.2010.5674772",

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AU - Kim, Woo Chan

AU - Lee, Kang Hoon

AU - Shin, Kyung Seop

AU - You, Ri Na

AU - Shin, Hyeon Seok

AU - Lee, Young Kwan

AU - Cho, Kiho

AU - Cho, Dong Ho

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AB - Genes are reported to constitute only 2-3% of the human genome, whereas repetitive elements (REs)make up a large portion of genomes of human and other eukaryotes. However, existing algorithms or tools for identification of REs as well as biological researches focus on the known specific REs. Thus, we design and implement a tool for unbiased mining of REs for large size genomes, called REMiner, in this paper. REMiner provides fast computation with low memory usage for the huge size of input genomic data. We show some interesting repeat patterns of the human chromosomes, which have not yet been reported. This chromosome-wide survey of complex, but highly-ordered RE array, will provide a foundation for a novel investigation into the genome.

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Unbiased mining tool of repetitive elements and their arrangement structure for large size genomes

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