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Proposal of Smith-Waterman algorithm on FPGA to accelerate the forward and backtracking steps

Author

Listed:
  • Fabio F de Oliveira
  • Leonardo A Dias
  • Marcelo A C Fernandes

Abstract

In bioinformatics, alignment is an essential technique for finding similarities between biological sequences. Usually, the alignment is performed with the Smith-Waterman (SW) algorithm, a well-known sequence alignment technique of high-level precision based on dynamic programming. However, given the massive data volume in biological databases and their continuous exponential increase, high-speed data processing is necessary. Therefore, this work proposes a parallel hardware design for the SW algorithm with a systolic array structure to accelerate the forward and backtracking steps. For this purpose, the architecture calculates and stores the paths in the forward stage for pre-organizing the alignment, which reduces the complexity of the backtracking stage. The backtracking starts from the maximum score position in the matrix and generates the optimal SW sequence alignment path. The architecture was validated on Field-Programmable Gate Array (FPGA), and synthesis analyses have shown that the proposed design reaches up to 79.5 Giga Cell Updates per Second (GCPUS).

Suggested Citation

  • Fabio F de Oliveira & Leonardo A Dias & Marcelo A C Fernandes, 2022. "Proposal of Smith-Waterman algorithm on FPGA to accelerate the forward and backtracking steps," PLOS ONE, Public Library of Science, vol. 17(6), pages 1-28, June.
    • Handle: RePEc:plo:pone00:0254736
    DOI: 10.1371/journal.pone.0254736
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    1. Danielle Miller & Michael A. Martin & Noam Harel & Omer Tirosh & Talia Kustin & Moran Meir & Nadav Sorek & Shiraz Gefen-Halevi & Sharon Amit & Olesya Vorontsov & Avraham Shaag & Dana Wolf & Avi Peretz, 2020. "Full genome viral sequences inform patterns of SARS-CoV-2 spread into and within Israel," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
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