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BMCBI
2007

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

13 years 10 months ago
160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA)
Background: 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. Results: In this paper, we focused on accelerating the Smith-Waterman algorithm by using FPGAbased 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. Conclusion: This design of FPGA accelerated hardware offers a new promising direction to seeking computation improvement of genomic database searching. Background The Smit...
Isaac T. S. Li, Warren Shum, Kevin Truong
Added 09 Dec 2010
Updated 09 Dec 2010
Type Journal
Year 2007
Where BMCBI
Authors Isaac T. S. Li, Warren Shum, Kevin Truong
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