NDLI: Parallel processing in biological sequence comparison using general purpose processors

Content Provider	IEEE Xplore Digital Library
Author	Sanchez, F. Salami, E. Ramirez, A. Valero, M.
Copyright Year	2005
Description	Author affiliation: HiPEAC Eur. Network of Excellence, Univ. Politecnica de Catalunya, Barcelona, Spain (Sanchez, F.; Salami, E.; Ramirez, A.; Valero, M.)
Abstract	The comparison and alignment of DNA and protein sequences are important tasks in molecular biology and bioinformatics. One of the most well known algorithms to perform the string-matching operation present in these tasks is the Smith-Waterman algorithm (SW). However, it is a computation intensive algorithm, and many researchers have developed heuristic strategies to avoid using it, specially when using large databases to perform the search. There are several efficient implementations of the SW algorithm on general purpose processors. These implementations try to extract data-level parallelism taking advantage of single-instruction multiple-data extensions (SIMD), capable of performing several operations in parallel on a set of data. In this paper, we propose a more efficient data parallel implementation of the SW algorithm. Our proposed implementation obtains a 30% reduction in the execution time relative to the previous best data-parallel alternative. In this paper we review different alternative implementation of the SW algorithm, compare them with our proposal, and present preliminary results for some heuristic implementations. Finally, we present a detailed study of the computational complexity of the different alignment algorithms presented and their behavior on the different aspect of the CPU microarchitecture.
Sponsorship	IEEE Comput. Soc. Tech. Comm. on Comput. Archit
Starting Page	99
Ending Page	108
File Size	806389
Page Count	10
File Format	PDF
ISBN	0780394615
DOI	10.1109/IISWC.2005.1526005
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2005-10-06
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Parallel processing Sequences DNA Proteins Bioinformatics Biology computing Databases Data mining Proposals Computational complexity
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
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
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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