SIMD Implementation of Modified Zhang’s Three-Frame Alignment Algorithm

Gene expression involves the alignment of organisms to understand their genetic information. DNA to protein alignment is the important first step in gene expression which involves alignment of DNA sequence to a reference genome. However, protein alignment algorithms are implemented sequentially via recurrence relation. Thus, making alignment slow. This paper discusses an SIMD implementation of a DNA to protein alignment algorithm using AVX2 instructions to speedup implementation. Result shows a speedup ranging from 1. 81x to 6. 1x as compared to sequential implementation.