Presentation | 2019-07-25 Acceleration of Human Genome Phenotypic Analysis using Bit-Parallel Search and Multiprocessing Yuichiro Miyamoto, Masao Okita, Fumihiko Ino, |
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PDF Download Page | PDF download Page Link |
Abstract(in Japanese) | (See Japanese page) |
Abstract(in English) | In this paper, we propose a combined method of a bit-parallel search in a base sequence and multiprocessing of t-tests for accelerating a phenotypic analysis of monozygotic twins based on a combination of Single Nucleotide Polymorphism (SNPs) and methylation sites. The phenotypic analysis consists of the following two processes: identification of neighboring pairs of SNP and methylation site in a base sequence over 3 billion bases, and t-tests on the pairs. The proposed method searches for neighboring pairs every 64 bases in a bit-parallel manner. In addition, the proposed method accelerates multiple t-tests using a multiprocessing paradigm. The experimental results show the proposed method was 46 times faster than the existing method on a 20-core CPU. |
Keyword(in Japanese) | (See Japanese page) |
Keyword(in English) | bioinformatics / range search / t-test / load balancing |
Paper # | CPSY2019-25,DC2019-25 |
Date of Issue | 2019-07-17 (CPSY, DC) |
Conference Information | |
Committee | CPSY / DC / IPSJ-ARC |
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Conference Date | 2019/7/24(3days) |
Place (in Japanese) | (See Japanese page) |
Place (in English) | Kitami Civic Hall |
Topics (in Japanese) | (See Japanese page) |
Topics (in English) | Parallel, Distributed and Cooperative Processing Systems and Dependable Computing |
Chair | Hidetsugu Irie(Univ. of Tokyo) / Satoshi Fukumoto(Tokyo Metropolitan Univ.) / Hiroshi Inoue(Kyushu Univ.) |
Vice Chair | Michihiro Koibuchi(NII) / Kota Nakajima(Fujitsu Lab.) / Hiroshi Takahashi(Ehime Univ.) |
Secretary | Michihiro Koibuchi(Nagoya Inst. of Tech.) / Kota Nakajima(Hokkaido Univ.) / Hiroshi Takahashi(Nihon Univ.) / (Chiba Univ.) |
Assistant | Eiji Arima(Univ. of Tokyo) / Shugo Ogawa(Hitachi) |
Paper Information | |
Registration To | Technical Committee on Computer Systems / Technical Committee on Dependable Computing / Special Interest Group on System Architecture |
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Language | JPN |
Title (in Japanese) | (See Japanese page) |
Sub Title (in Japanese) | (See Japanese page) |
Title (in English) | Acceleration of Human Genome Phenotypic Analysis using Bit-Parallel Search and Multiprocessing |
Sub Title (in English) | |
Keyword(1) | bioinformatics |
Keyword(2) | range search |
Keyword(3) | t-test |
Keyword(4) | load balancing |
1st Author's Name | Yuichiro Miyamoto |
1st Author's Affiliation | Osaka University(Osaka Univ.) |
2nd Author's Name | Masao Okita |
2nd Author's Affiliation | Osaka University(Osaka Univ.) |
3rd Author's Name | Fumihiko Ino |
3rd Author's Affiliation | Osaka University(Osaka Univ.) |
Date | 2019-07-25 |
Paper # | CPSY2019-25,DC2019-25 |
Volume (vol) | vol.119 |
Number (no) | CPSY-147,DC-148 |
Page | pp.pp.117-122(CPSY), pp.117-122(DC), |
#Pages | 6 |
Date of Issue | 2019-07-17 (CPSY, DC) |