Performance Analysis of DNA Sequencing Using Smith-Waterman Algorithm on FPGA

Abstract

The Smith-Waterman algorithm is the most accurate and optimal alignment algorithm for DNA sequencing. It is utilized to locate the ideal local alignment between two sequences. While looking sequence databases that may contain billions of sequences, this algorithm turns out to be computationally costly and tedious. Smith-Waterman algorithm needs additional memory space and this constrains the extent of a sequence to be aligned. In this study we will implement the S-W algorithm on a FPGA board which will speed up the performance execution of the program with less utilization and more efficiency. Keywords: Bioinformatics, sequence alignment, dynamic programming, Smith-Waterman algorithm, FPGA Cite this Article Anna Hakim, Anam Kashtwari, Rajinder Tiwari, Jamini Sharma. Performance Analysis of DNA Sequencing Using Smith-Waterman Algorithm on FPGA. Journal of VLSI Design Tools & Technology. 2019; 9(2): 9–13p.