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2014-03-10 - Colloque/Article dans les actes avec comité de lecture - Anglais - 6 page(s)

Chang Xin, Escobar Juzga Fernando, Valderrama Carlos , Vincent Robert, "Optimization Strategies for Smith-Waterman Algorithm on FPGA platform" in Proceedings - 2014 International Conference on Computational Science and Computational Intelligence, CSCI 2014, Volume 1, 2014, 9-14, Las Vegas, NV, United States, 2014

  • Codes CREF : Electronique et électrotechnique (DI2411)
  • Unités de recherche UMONS : FPMs - Service du Doyen (F100)

Abstract(s) :

(Anglais) With the rapid development of the new generation of DNA sequencers, the rate of data generation is rapidly outpacing the rate at which it can be computationally processed. Traditional sequence alignment based on PC cannot meet this growing demand. Accelerate the algorithm execution using reconfigurable architectures such as FPGAs provides better performance compared to other platforms. This paper contributes to the dynamic programming of sequence alignment and the implementation of the Smith-Waterman algorithm on FPGA. In addition, we provide a comparative analysis of the various optimization strategies of the Smith-Waterman algorithm. This work will provide a path for a major acceleration of sequence alignment on FPGA platforms. © 2014 IEEE.

Identifiants :
  • ISBN : 978-147993009-8
  • DOI : 10.1109/CSCI.2014.10