Journal
BIOINFORMATICS
Volume 30, Issue 22, Pages 3166-3173Publisher
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/btu507
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Funding
- National Science Foundation [IIS-1017621, DGE-0654108]
- Direct For Computer & Info Scie & Enginr
- Div Of Information & Intelligent Systems [1017621] Funding Source: National Science Foundation
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Motivation: Mapping of high-throughput sequencing data and other bulk sequence comparison applications have motivated a search for high-efficiency sequence alignment algorithms. The bit-parallel approach represents individual cells in an alignment scoring matrix as bits in computer words and emulates the calculation of scores by a series of logic operations composed of AND, OR, XOR, complement, shift and addition. Bit-parallelism has been successfully applied to the longest common subsequence (LCS) and edit-distance problems, producing fast algorithms in practice. Results: We have developed BitPAl, a bit-parallel algorithm for general, integer-scoring global alignment. Integer-scoring schemes assign integer weights for match, mismatch and insertion/deletion. The BitPAl method uses structural properties in the relationship between adjacent scores in the scoring matrix to construct classes of efficient algorithms, each designed for a particular set of weights. In timed tests, we show that BitPAl runs 7-25 times faster than a standard iterative algorithm.
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