Abstract
Mapping of next-generation sequencing data and other pro-cessor-intensive sequence comparison applications have motivated a continued search for high efficiency sequence alignment algorithms. In one approach, which exploits the inherent parallelism in computer logic calculations, individual cells in an alignment scoring matrix are represented as bits in a computer word and the calculation of scores is emulated by a series of bit operations comprised 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 solutions which are significantly faster than standard implementations. But, the intensive mental effort required to produce these solutions, which are closely tied to special properties of the problems, has limited efforts to extend bit-parallelism to more general scoring schemes. In this paper, we give the first bit-parallel solution for general, integer-scoring global alignment. Integer-scoring schemes, which are widely used, assign integer weights for match, mismatch, and insertion/deletion or indel. Our method depends on structural properties of the relationship between adjacent scores in the scoring matrix. We utilize these properties to construct a class of efficient algorithms, each designed for a particular set of weights, and we introduce a standard for characterizing the efficiency in terms of the average number of bit-operations per cell of the original scoring matrix.
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References
Allison, L., Dix, T.I.: A bit-string longest-common-subsequence algorithm. Information Processing Letters 23(5), 305–310 (1986)
Bergeron, A., Hamel, S.: Vector algorithms for approximate string matching. International Journal of Foundations of Computer Science 13(01), 53–65 (2002)
Crochemore, M., Iliopoulos, C.S., Pinzon, Y.J., Reid, J.F.: A fast and practical bit-vector algorithm for the longest common subsequence problem. Information Processing Letters 80(6), 279–285 (2001)
Gelfand, Y., Loving, J., Hernandez, Y., Benson, G.: VNTRseek – A Computational Pipeline to Detect Tandem Repeat Variants in Next-Generation Sequencing Data: Analysis of the 454 Watson Genome. In: Proc. of RECOMB-seq: The Third Annual RECOMB Satellite Workshop on Massively Parallel Sequencing (to appear, 2013)
Hyyrö, H.: Bit-parallel LCS-length computation revisited. In: Proc. 15th Australasian Workshop on Combinatorial Algorithms, AWOCA 2004 (2004)
Hyyrö, H., Fredriksson, K., Navarro, G.: Increased bit-parallelism for approximate and multiple string matching. Journal of Experimental Algorithmics (JEA) 10, 2–6 (2005)
Kernighan, B.W., Ritchie, D.M.: The C programming language, 2nd edn. Prentice Hall (1988)
Myers, G.: A fast bit-vector algorithm for approximate string matching based on dynamic programming. Journal of the ACM (JACM) 46(3), 395–415 (1999)
Navarro, G.: Approximate regular expression searching with arbitrary integer weights. Nordic Journal of Computing 11(4), 356–373 (2004)
Needleman, S., Wunch, C.: A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443–453 (1970)
Smith, T.F., Waterman, M.S.: Identification of common molecular subsequences. Journal of Molecular Biology 147(1), 195–197 (1981)
Wu, S., Manber, U.: Fast text searching: allowing errors. Communications of the ACM 35(10), 83–91 (1992)
Wu, S., Manber, U., Myers, G.: A subquadratic algorithm for approximate limited expression matching. Algorithmica 15(1), 50–67 (1996)
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Benson, G., Hernandez, Y., Loving, J. (2013). A Bit-Parallel, General Integer-Scoring Sequence Alignment Algorithm. In: Fischer, J., Sanders, P. (eds) Combinatorial Pattern Matching. CPM 2013. Lecture Notes in Computer Science, vol 7922. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-38905-4_7
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DOI: https://doi.org/10.1007/978-3-642-38905-4_7
Publisher Name: Springer, Berlin, Heidelberg
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