No abstract

BLAST adopts index-based approach to detect the matches between two substrings by looking up a large table and processing one match per query. In this paper, we propose a systolic array approach to detect string matches without using looking up tables. The pipelining systolic array is implemented as a multi-seeds detection and parallel extension engine to accelerate the first two stages of NCBI BLAST algorithm. Different from the index-based approach, our implementation consumes little memory resources and eliminates redundant string extensions. Our FPGA implementation achieves superior performance results in both of processing element number and clock frequency over related works in the area of FPGA BLAST accelerators. The experimental results show a speedup factor of more than 20× over the NCBI BLAST software running on a current mainstream PC platform.