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Open Access Methodology article

160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA)

Isaac TS Li1, Warren Shum2 and Kevin Truong12*

Author Affiliations

1 Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, Ontario, M5S 3G9, Canada

2 Edward S. Rogers Sr. Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Circle, Toronto, Ontario, M5S 3G4, Canada

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BMC Bioinformatics 2007, 8:185  doi:10.1186/1471-2105-8-185

Published: 7 June 2007



To infer homology and subsequently gene function, the Smith-Waterman (SW) algorithm is used to find the optimal local alignment between two sequences. When searching sequence databases that may contain hundreds of millions of sequences, this algorithm becomes computationally expensive.


In this paper, we focused on accelerating the Smith-Waterman algorithm by using FPGA-based hardware that implemented a module for computing the score of a single cell of the SW matrix. Then using a grid of this module, the entire SW matrix was computed at the speed of field propagation through the FPGA circuit. These modifications dramatically accelerated the algorithm's computation time by up to 160 folds compared to a pure software implementation running on the same FPGA with an Altera Nios II softprocessor.


This design of FPGA accelerated hardware offers a new promising direction to seeking computation improvement of genomic database searching.