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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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
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
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)