The Implementation and Analysis of Smith-Waterman Algorithm on Systolic Array
Wang Dong · Chinese Journal of Computers · 2004
Smith Waterman algorithm is a classical sequence alignment algorithm and behaves very well in a bi sequence alignment. But its performance is not satisfying when aligning a lot of sequences. The systolic array architecture shows good fitness for the algorithm. By appending the array as a co processor to the Godson 1 architecture, authors build the hardware model of the accelerator. By comparing the performance on the Godson 1 simulator with the co processor and the one without, the systolic array shows almost linear speed up on the algorithm. Authors at last analyze the model and performance data to reveal the aspects that affect the performance especially the cells’ number, the sequences’ length, branches and cache size.