FPGA-based Scalable Implementation of the General Smith-Waterman Algorithm

O. Creţ, Ş. Mathe, B. Szente, Z. Mathe, C. Vancea, F. Rusu, and A. Dǎrǎbant (Romania)


Smith-Waterman algorithm, systolic architecture, FPGA, VHDL, Bioinformatics.


The Smith-Waterman algorithm is fundamental in Bioinformatics. This paper presents an FPGA-based systolic implementation of the Smith-Waterman algorithm that addresses a general case of it. A solution that improves the scalability of the design is proposed. The architecture is optimized for both speed and space, by reusing the hardware resources for the two main phases: Initialization of the systolic array and Computation. The performance estimation formulas are presented and used to prove the system's efficiency. The design was developed in VHDL and tested on Xilinx Virtex family FPGAs, for different sizes of the systolic array and different speed grades of the devices. The obtained results prove the efficiency of the proposed architecture.

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