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arXiv · 1909.00899

De(con)struction of the lazy-F loop: improving performance of Smith Waterman alignment

Roman Snytsar
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Abstract

Striped variation of the Smith-Waterman algorithm is known as extremely efficient and easily adaptable for the SIMD architectures. However, the potential for improvement has not been exhausted yet. The popular Lazy-F loop heuristic requires additional memory access operations, and the worst-case performance of the loop could be as bad as the nonvectorized version. We demonstrate the progression of the lazy-F loop transformations that improve the loop performance, and ultimately eliminate the loop completely. Our algorithm achieves the best asymptotic performance of all scan-based SW algorithms O(n/p+log(p)), and is very efficient in practice.

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Roman Snytsar. 2019-09-03. De(con)struction of the lazy-F loop: improving performance of Smith Waterman alignment. https://arxiv.org/abs/1909.00899

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