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