An Extended Instruction Set for Bioinformatics’ Multiple Sequence Alignment †

Abstract

Multiple Sequence Alignment (MSA) is one of the most fundamental methodologies in Bioinformatics and the method capable of arranging DNA or protein sequences to detect regions of similarity. Even on cutting-edge workstations, the MSA procedure requires a significant amount of time regarding its execution time. This paper demonstrates how to utilize Extensa Explorer by Tensilica (Cadence) to create an extended instruction set to meet the requirements of some of the most widely used algorithms in Bioinformatics for MSA analysis. Kalign showed the highest acceleration, reducing Instruction Fetches (IF) and Execution Time (ET) by 30.29 and 43.49 percent, respectively. Clustal had acceleration of 14.2% in IF and 17.9% in ET, whereas Blast had 12.35% in IF and 16.25% in ET. © 2022 by the authors.