Hardware implementation of the Smith-Waterman Algorithm using Recursive Variable Expansion

摘要

In this paper we adapted a novel approach for accelerating the Smith-Waterman (S-W) algorithm using Recursive Variable Expansion (RVE), which exposes extra parallelism in the algorithm, as compared to any other technique. The results demonstrate that applying the recursive variable expansion technique speeds up the performance by a factor of 1.36 to 1.41, as compared to traditional acceleration approaches at the cost of using 1.25 to 1.28 times more hardware resources.