Time Improvement of Smith-Waterman Algorithm Using OpenMP and SIMD

Abstract

Sequence alignment is a problem in bioinformatics that involves arranging sequences of proteins, RNA or DNA so that similar regions between two or more sequences may be determined. The Smith-Waterman algorithm is a key algorithm for aligning sequences. This paper uses the OpenMP application-programming interface along with the Single-Instruction Multiple-Data (SIMD) instructions. Advanced Vector Instructions 2 (AVX2) is used to implement the SIMD paradigm. It utilizes both fine-level and coarse-level parallelism to improve resource utilization without requiring support from multiple nodes in a distributed memory system. The algorithm shows a multifold decrease in execution time in comparison to an implementation that is sequentially executed.