BitPAl: a bit-parallel, general integer-scoring sequence alignment algorithm
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 emulate...
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| Vydané v: | Bioinformatics (Oxford, England) Ročník 30; číslo 22; s. 3166 - 3173 |
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| Hlavní autori: | , , |
| Médium: | Journal Article |
| Jazyk: | English |
| Vydavateľské údaje: |
England
Oxford University Press
15.11.2014
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| Predmet: | |
| ISSN: | 1367-4803, 1367-4811, 1367-4811 |
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| Shrnutí: | 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.
Availability and implementation: Source code is freely available for download at http://lobstah.bu.edu/BitPAl/BitPAl.html . BitPAl is implemented in C and runs on all major operating systems.
Contact : jloving@bu.edu or yhernand@bu.edu or gbenson@bu.edu
Supplementary information : Supplementary data are available at Bioinformatics online. |
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| Bibliografia: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Associate Editor: John Hancock |
| ISSN: | 1367-4803 1367-4811 1367-4811 |
| DOI: | 10.1093/bioinformatics/btu507 |