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.
Highlights
Deoxyribonucleic Acid (DNA) is made up of thymine (T), guanine (G), cytosine (C) and adenine (A) nucleotides (NTs)[1]
Field Programmable Gate Array (FPGA) are attractive platforms to speed up DNA sequence alignment computation compared to General Purpose Processor (GPP)
A more complex SW algorithm was introduced by Gotoh which is suitable for the affine gaps due to mutation in DNA sequence [16] as shown in (1)
Summary
DNA is made up of thymine (T), guanine (G), cytosine (C) and adenine (A) nucleotides (NTs)[1]. The sequence alignment algorithm can be implemented in SA to speed up its computation time and uses FPGA to improve the DNA sequencer computation process. The implementation of FPGA related to DNA sequence alignment architectures are extensively reported in [9], [10], [11], [12], [13] and [14] All of these architectures are designed based on SA with realization of the SW algorithm with linear gap penalty. The highest score will be the highest value among its neighbouring cells (top, left, diagonal)
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