Abstract
Searching a database for a local alignment to a query under a typical scoring scheme such as PAM120 or BLOSUM62, is a computation that has resisted algorithmic improvement due to its basis in dynamic programming and the weak nature of the signals being searched for. In a query preprocessing step, a set of tables can be built that permit one to (a) eliminate a large fraction of the dynamic programming matrix from consideration, and (b) to compute several steps of the remainder with a single table lookup. While this result is not an asymptotic improvement over the original Smith-Waterman algorithm, its complexity is characterized in terms of some sparse features of the matrix and it does yields 3.33 factor improvement over the basic algorithm in practice.
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References
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© 2002 Springer-Verlag Berlin Heidelberg
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Myers, G., Durbin, R. (2002). Invited Lecture — Accelerating Smith-Waterman Searches. In: Guigó, R., Gusfield, D. (eds) Algorithms in Bioinformatics. WABI 2002. Lecture Notes in Computer Science, vol 2452. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45784-4_25
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DOI: https://doi.org/10.1007/3-540-45784-4_25
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