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Paper Abstract and Keywords
Presentation 2011-11-30 09:00
An Acceleration Method for Three-Dimensional Smith-Waterman Algorithm on a GPU
Saori Sudo, Masato Yoshimi, Mitsunori Miki (Doshisha Univ.) CPSY2011-49
Abstract (in Japanese) (See Japanese page) 
(in English) Graphic processing units (GPUs), which was entirely used in image processing, have been applied to a lot of studies and products in general purpose computation. One of the most famous algorithm expected to accel- erate by utilizing GPU is Smith-Waterman (SW) algorithm in bioinformatics. The algorithm computes sequence alignment obtains the most similar part of strings and patterns between a pair of DNA sequences. As the application of SW method, a study to analyze time series data of fNIRS, which measures cerebral blood flows is progressing. Two challenges are required to analyze time series data from dozens of channels by SW method; extension of se- ries analyzed simultaneously and relaxation of computing amount. This paper proposes the three-dimensional SW (3D-SW) method as evaluation of GPU implementation to confirm achieving high-performance compared to CPU implementation.
Keyword (in Japanese) (See Japanese page) 
(in English) GPU / Smith-Waterman algorithm / Parallel Computing / / / / /  
Reference Info. IEICE Tech. Rep., vol. 111, no. 328, CPSY2011-49, pp. 35-40, Nov. 2011.
Paper # CPSY2011-49 
Date of Issue 2011-11-22 (CPSY) 
ISSN Print edition: ISSN 0913-5685    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)
Download PDF CPSY2011-49

Conference Information
Committee VLD DC IPSJ-SLDM CPSY RECONF ICD CPM  
Conference Date 2011-11-28 - 2011-11-30 
Place (in Japanese) (See Japanese page) 
Place (in English) NewWelCity Miyazaki 
Topics (in Japanese) (See Japanese page) 
Topics (in English) Design Gaia 2010 -New Field of VLSI Design- 
Paper Information
Registration To CPSY 
Conference Code 2011-11-VLD-DC-SLDM-CPSY-RECONF-ICD-CPM 
Language Japanese 
Title (in Japanese) (See Japanese page) 
Sub Title (in Japanese) (See Japanese page) 
Title (in English) An Acceleration Method for Three-Dimensional Smith-Waterman Algorithm on a GPU 
Sub Title (in English)  
Keyword(1) GPU  
Keyword(2) Smith-Waterman algorithm  
Keyword(3) Parallel Computing  
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1st Author's Name Saori Sudo  
1st Author's Affiliation Doshisha University (Doshisha Univ.)
2nd Author's Name Masato Yoshimi  
2nd Author's Affiliation Doshisha University (Doshisha Univ.)
3rd Author's Name Mitsunori Miki  
3rd Author's Affiliation Doshisha University (Doshisha Univ.)
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Speaker Author-1 
Date Time 2011-11-30 09:00:00 
Presentation Time 25 minutes 
Registration for CPSY 
Paper # CPSY2011-49 
Volume (vol) vol.111 
Number (no) no.328 
Page pp.35-40 
#Pages 6 
Date of Issue 2011-11-22 (CPSY) 

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