Reconfigurable accelerator for the word-matching stage of BLASTN

  • Authors:

  • Yupeng Chen;Bertil Schmidt;Douglas L. Maskell

  • Affiliations:

  • School of Computer Engineering, Nanyang Technological University, Singapore;Institut fuer Informatik, Johannes Gutenberg University, Germany;School of Computer Engineering, Nanyang Technological University, Singapore

  • Venue:
  • IEEE Transactions on Very Large Scale Integration (VLSI) Systems
  • Year:
  • 2013

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Abstract

BLAST is one of the most popular sequence analysis tools used by molecular biologists. It is designed to efficiently find similar regions between two sequences that have biological significance. However, because the size of genomic databases is growing rapidly, the computation time of BLAST, when performing a complete genomic database search, is continuously increasing. Thus, there is a clear need to accelerate this process. In this paper, we present a new approach for genomic sequence database scanning utilizing reconfigurable field programmable gate array (FPGA)-based hardware. In order to derive an efficient structure for BLASTN, we propose a reconfigurable architecture to accelerate the computation of the word-matching stage. The experimental results show that the FPGA implementation achieves a speedup around one order of magnitude compared to the NCBI BLASTN software running on a general purpose computer.