NDLI: GPU-accelerated Burrow-Wheeler Transform for genomic data

Content Provider	IEEE Xplore Digital Library
Author	Zhiheng Zhao Jianping Yin Wei Xiong
Copyright Year	2012
Description	Author affiliation: Sch. of Comput. Sci., Nat. Univ. of Defense Technol., Changsha, China (Zhiheng Zhao; Jianping Yin; Wei Xiong)
Abstract	As the core of FM-index and compressed suffix array, the Burrows-Wheeler Transform (BWT) plays a key role in indexing genomic sequence data for pattern search. It is more space-efficient than suffix tree and suffix array and also has good searching performance. However, computing a BWT from a sequence in efficient space and time is challenging. In this article, we present a fast algorithm for computing BWT which leverages the computing power of graphics processing unit (GPU). It is based on a blockwise suffix sorting method which builds BWT block-by-block and uses a GPU to accelerate the suffix sorting procedures. Our GPU-accelerated algorithm only needs small memory space and experiments show that it is about 16 times faster than the original CPU implementation for computing BWT of human whole genome.
Starting Page	889
Ending Page	892
File Size	376162
Page Count	4
File Format	PDF
ISBN	9781467311830
e-ISBN	9781467311847
DOI	10.1109/BMEI.2012.6513199
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2012-10-16
Publisher Place	China
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	suffix array Burrows-Wheeler Transform GPU
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
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3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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