High Performance Systolic Array Core Architecture Design for DNA Sequencer

¹ The Integrated Circuits and Systems Design Group (ICASe),School of Microelectronic Engineering, Universiti Malaysia Perlis, Pauh Putra Campus, 02600, Arau, Perlis, Malaysia.
² School of Computer and Communication Engineering, Universiti Malaysia Perlis, Pauh Putra Campus, 02600, Arau, Perlis, Malaysia.

^* Corresponding author: nazrin@unimap.edu.my

Abstract

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.