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 and 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) |
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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) |
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bioinformatics |
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range search |
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t-test |
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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 |
6 |
Date of Issue |
2019-07-17 (CPSY, DC) |
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