NDLI: Parallel biological sequence comparison using prefix computations

Content Provider	IEEE Xplore Digital Library
Author	Aluru, S. Futamura, N. Mehrotra, K.
Copyright Year	1999
Description	Author affiliation: Dept. of Comput. Sci., New Mexico State Univ., Las Cruces, NM, USA (Aluru, S.)
Abstract	We present practical parallel algorithms using prefix computations for various problems that arise in pairwise comparison of biological sequences. We consider both constant and affine gap penalty functions, full-sequence and subsequence matching and space-saving algorithms. The best known sequential algorithms solve these problems in O(mn) time and O(m+n) space, where m and n are the lengths of the two sequences. All the algorithms presented in this paper are time optimal with respect to the best known sequential algorithms and can use O(n/log n) processors where n is the length of the larger sequence. While optimal parallel algorithms for many of these problems are known, we use a simple framework and demonstrate how these problems can be solved systematically using repeated parallel prefix operations. We also present a space-saving algorithm that uses O(m+n/p) space and runs in optimal time where p is the number of the processors used.
Starting Page	653
Ending Page	659
File Size	135529
Page Count	7
File Format	PDF
ISBN	0769501435
DOI	10.1109/IPPS.1999.760546
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	1999-04-12
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Biology computing Concurrent computing Sequences Computer science Stacking Engineering profession Parallel algorithms Dynamic programming Runtime Costs
Content Type	Text
Resource Type	Article

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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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