MATEC Web of Conferences (Jan 2018)

High Performance Systolic Array Core Architecture Design for DNA Sequencer

  • Saiful Nurdin Dayana,
  • Md. Isa Mohd. Nazrin,
  • Che Ismail Rizalafande,
  • Imran Ahmad Muhammad

DOI
https://doi.org/10.1051/matecconf/201815006009
Journal volume & issue
Vol. 150
p. 06009

Abstract

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This paper presents a high performance systolic array (SA) core architecture design for Deoxyribonucleic Acid (DNA) sequencer. The core implements the affine gap penalty score Smith-Waterman (SW) algorithm. This time-consuming local alignment algorithm guarantees optimal alignment between DNA sequences, but it requires quadratic computation time when performed on standard desktop computers. The use of linear SA decreases the time complexity from quadratic to linear. In addition, with the exponential growth of DNA databases, the SA architecture is used to overcome the timing issue. In this work, the SW algorithm has been captured using Verilog Hardware Description Language (HDL) and simulated using Xilinx ISIM simulator. The proposed design has been implemented in Xilinx Virtex -6 Field Programmable Gate Array (FPGA) and improved in the core area by 90% reduction.