NDLI: Z-align: An Exact and Parallel Strategy for Local Biological Sequence Alignment in User-Restricted Memory Space

Content Provider	IEEE Xplore Digital Library
Author	Batista, R.B. de Melo, A.C.M.A.
Copyright Year	2006
Description	Author affiliation: Dept. of Comput. Sci., Brasilia Univ. (Batista, R.B.; de Melo, A.C.M.A.)
Abstract	The algorithm proposed by Smith-Waterman is an exact method that obtains optimal local alignments in quadratic space and time. For long sequences, quadratic complexity makes the use of this algorithm impractical. In this scenario, parallel computing is a very attractive alternative. In this paper, we propose and evaluate z-align, a parallel exact strategy based on the divergence concept to locally align long biological sequences using an affine gap function. Z-align runs in limited memory space, where the amount of memory used can be defined by the user. The results collected in a cluster with 16 processors presented very good speedups for long real DNA sequences. By comparing the results obtained with z-align and BLAST, it is clear that z-align is able to produce longer and more significant alignments
Starting Page	1
Ending Page	10
File Size	454952
Page Count	10
File Format	PDF
ISBN	1424403278
ISSN	15525244
DOI	10.1109/CLUSTR.2006.311858
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2006-09-25
Publisher Place	Spain
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Sequences DNA Parallel processing Biological system modeling Dynamic programming Pattern matching Genomics Bioinformatics Organisms Biology
Content Type	Text
Resource Type	Article

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