Systolic processing element based on the Viterbi algorithm for DNA sequence alignment

Abstract

This paper presents the potential of the one-dimensional systolic processing element of the Viterbi algorithm in optimizing the DNA sequence alignment system processing engine. The objective of this paper was to optimize the sensitive DNA sequence alignment algorithm toward improving the performance and design complexity. In addition, theoretical study, design, and simulation were conducted using the Altera Quartus II version 9.1 software. The proposed architecture has been tested and is capable of accelerating more than 32 bits of input. As a conclusion, the proposed systolic design has been proven and is able to optimize the performance and design complexity of the most sensitive DNA sequence alignment algorithm on hardware-based accelerator platform.