Optimization Strategies for Smith-Waterman Algorithm on FPGA Platform

With the rapid development of the new generation of DNA sequencers, the rate of data generation is rapidly outpacing the rate at which it can be computationally processed. Traditional sequence alignment based on PC cannot meet this growing demand. Accelerate the algorithm execution using reconfigurable architectures such as FPGAs provides better performance compared to other platforms. This paper contributes to the dynamic programming of sequence alignment and the implementation of the Smith-Waterman algorithm on FPGA. In addition, we provide a comparative analysis of the various optimization strategies of the Smith-Waterman algorithm. This work will provide a path for a major acceleration of sequence alignment on FPGA platforms.