CS3211 Parallel & Concurrent Programming AY18/19 Sem 2 Project 2
Project Members: Alvin Yan, Au Liang Jun, Michael Hu
The Smith-Waterman algorithm is a dynamic algorithm used for local sequence alignment of 2 strings, commonly used for nucleic acid sequences or protein sequences. In this project, we strive to parallelise the Smith-Waterman algorithm in an exercise of implementing concurrency and a study of its challenges.
To draw insights on speedup, an implementation of the original sequential algorithm was also written. To reduce runtime of our code, we utilised memoization based off known formulas modelling the affine gap, the gap penalty used in the algorithm. All code was written in the x10 programming language.