Fast Smith-Waterman hardware implementation

Abstract—The Smith-Waterman (SW) algorithm is one of the widely used algorithms for sequence alignment in computational biology. With the growing size of the sequence database, there is always a need for even faster implementation of SW. In this paper, we have implemented two Recursive Variable Expansion (RVE) based techniques, which are proved to give better speedup than any best dataflow approach at the cost of extra area. Compared to dataflow approach, our HW implementation is 2.29 times faster at the expense of 2.82 times more area. Keywords-computational biology; sequence alignment; hardware acceleration; RVE I