MATEC Web Conf.
Volume 150, 2018Malaysia Technical Universities Conference on Engineering and Technology (MUCET 2017)
|Number of page(s)||6|
|Section||Information & Communication Technology (ICT), Science (SCI) & Mathematics (SM)|
|Published online||23 February 2018|
High Performance Systolic Array Core Architecture Design for DNA Sequencer
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: firstname.lastname@example.org
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.
© The Authors, published by EDP Sciences, 2018
This is an Open Access article distributed under the terms of the Creative Commons Attribution License 4.0, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (http://creativecommons.org/licenses/by/4.0/).
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