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Paper Abstract and Keywords
Presentation 2019-07-25 13:25
Acceleration of Human Genome Phenotypic Analysis using Bit-Parallel Search and Multiprocessing
Yuichiro Miyamoto, Masao Okita, Fumihiko Ino (Osaka Univ.) CPSY2019-25 DC2019-25
Abstract (in Japanese) (See Japanese page) 
(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) 
(in English) bioinformatics / range search / t-test / load balancing / / / /  
Reference Info. IEICE Tech. Rep., vol. 119, no. 147, CPSY2019-25, pp. 117-122, July 2019.
Paper # CPSY2019-25 
Date of Issue 2019-07-17 (CPSY, DC) 
ISSN Online edition: ISSN 2432-6380
Copyright
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reproduction
All rights are reserved and no part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopy, recording, or any information storage and retrieval system, without permission in writing from the publisher. Notwithstanding, instructors are permitted to photocopy isolated articles for noncommercial classroom use without fee. (License No.: 10GA0019/12GB0052/13GB0056/17GB0034/18GB0034)
Download PDF CPSY2019-25 DC2019-25

Conference Information
Committee CPSY DC IPSJ-ARC  
Conference Date 2019-07-24 - 2019-07-26 
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 
Paper Information
Registration To CPSY 
Conference Code 2019-07-CPSY-DC-ARC 
Language Japanese 
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  
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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.)
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Speaker Author-1 
Date Time 2019-07-25 13:25:00 
Presentation Time 30 minutes 
Registration for CPSY 
Paper # CPSY2019-25, DC2019-25 
Volume (vol) vol.119 
Number (no) no.147(CPSY), no.148(DC) 
Page pp.117-122 
#Pages
Date of Issue 2019-07-17 (CPSY, DC) 


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