Analysis of Repetition Structure in Huge Sequences
| Project/Area Number |
25280079
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| Research Category |
Grant-in-Aid for Scientific Research (B)
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| Allocation Type | Partial Multi-year Fund |
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| Section | 一般 |
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| Research Field |
Intelligent informatics
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| Research Institution | Hokkaido University |
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Principal Investigator |
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| Co-Investigator(Kenkyū-buntansha) |
KUDO Mineichi 北海道大学, 大学院情報科学研究科, 教授 (60205101)
TAKIGAWA Ichigaku 北海道大学, 大学院情報科学研究科, 准教授 (10374597)
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| Co-Investigator(Renkei-kenkyūsha) |
MAMITSUKA Hiroshi 京都大学, 化学研究所, 教授 (00346107)
KIDA Takuya 北海道大学, 大学院情報科学研究科, 准教授 (70343316)
OKUBO Yoshiaki 北海道大学, 大学院情報科学研究科, 助教 (40271639)
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| Project Period (FY) |
2013-04-01 – 2016-03-31
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| Project Status |
Completed (Fiscal Year 2015)
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| Budget Amount *help |
¥8,320,000 (Direct Cost: ¥6,400,000、Indirect Cost: ¥1,920,000)
Fiscal Year 2015: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
Fiscal Year 2014: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Fiscal Year 2013: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
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| Keywords | 知識発見とデータマイニング / シーケンスマイニング / ゲノム情報処理 / 頻出パターンマイニング |
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| Outline of Final Research Achievements |
We developed an algorithm for enumerating frequent approximate string patterns, and proposed a method of extracting occurrence regions of the enumerated patterns as a method of extracting interspersed repetitive elements in a huge sequence like a DNA sequence. Patterns of proposed methods have occurrences of clear boundaries, so there is little chance to count essentially the same region more than once. Furthermore, our enumeration algorithm runs very fast and with small memory. According to our empirical results using human chromosome 21, a half of the known Alu regions, which are famous interspersed repetitive elements, is extracted as occurrence regions of 100 representative patterns that were selected from enumerated frequent approximate patterns.
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Report
(4 results)
Research Products
(17 results)
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[Journal Article] Noise Free Multi-armed Bandit Game2016
Author(s)
Atsuyoshi Nakamura, David P. Helmbold, Manfred K. Warmuth
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Journal Title
Lecture Notes in Computer Science
Volume: 9618
Pages: 412-423
DOI
NAID
ISBN
9783319299990, 9783319300009
Related Report
Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
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[Journal Article] MED26 regulates the transcription of snRNA genes through the recruitment of little elongation complex2015
Author(s)
Takahashi, H., Takigawa, I., Watanabe, M., Anwar, D., Shibata, M., Tomomori-Sato, C., Sato, S., Ranjan, A., Seidel, C.W., Tsukiyama, T., Mizushima, W., Hayashi, M., Ohkawa, Y., Conaway, J.W., Conaway, R.C. and Hatakeyama, S
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Journal Title
Nature Commun.
Volume: 5
Issue: 1
Pages: 5941-5941
DOI
NAID
Related Report
Peer Reviewed / Open Access
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