An Algorithm for the Sequence Alignment with Gap Penalty Problem using Multiway Divide-and-Conquer and Matrix Transposition

We present a cache-efficient parallel algorithm for the sequence alignment with gap penalty problem for shared-memory machines using multiway divide-and-conquer and not-in-place matrix transposition. Our r-way divide-and-conquer algorithm, for a fixed natural number r >= 2, performs Theta (n(3)) work, achieves Theta (n(logr(2r-1))) span, and incurs O(n(3)/(BM) + (n(2)/B)log root M) serial cache misses for n > gamma M, and incurs O ((n(2)/B)log(n/root M)) serial cache misses for alpha root M < n <= gamma M, where, M is the cache size, B is the cache line size, and alpha and gamma are constants. Published by Elsevier B.V.