NDLI: Speeding Up Pairwise Sequence Alignments: A Scoring Scheme Reweighting Based Approach

Content Provider	IEEE Xplore Digital Library
Author	Yong Gao Henderson, M.
Copyright Year	2007
Description	Author affiliation: Univ. of British Columbia Okanagan, Kelowna (Yong Gao; Henderson, M.)
Abstract	A general technique based on scoring scheme reweighting is proposed that can be used to speed up dynamic programming algorithms for a variety of pairwise sequence alignment problems. For the standard sequence alignment problem with an arbitrary gap penalty function, we show that a reweighted scoring scheme can be obtained by an efficient preprocessing step that computes a set of upper bounds on the score of the optimal alignment between pairs of suffixes of the sequences. A series of experiments on synthetic sequences and biological sequences indicate that our algorithm offers significant and robust speedup over the standard cubic-time dynamic programming algorithm. For sequences of length up to 2000 used in our experiments, the speedup factor ranges from 4 to more than 50. With a strong upper bound, a sub-cubic behavior in running time is also observed for all the tested situations.
Starting Page	1194
Ending Page	1198
File Size	408451
Page Count	5
File Format	PDF
ISBN	9781424415090
DOI	10.1109/BIBE.2007.4375714
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2007-10-14
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Dynamic programming Heuristic algorithms Upper bound Computer science Art Biology computing Robustness Testing RNA
Content Type	Text
Resource Type	Article

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