Name
Title | ||
|---|---|---|
Improving the performance of the needleman-wunsch algorithm using parallelization and vectorization techniques |
Abstract | ||
|---|---|---|
The Needleman-Wunsch (NW) is a dynamic programming algorithm used in the pairwise global alignment of two biological sequences. In this paper, three sets of parallel implementations of the NW algorithm are presented using a mixture of specialized software and hardware solutions: POSIX Threads-based, SIMD Extensions-based and a GPU-based implementations. The three implementations aim at improving the performance of the NW algorithm on large scale input without affecting its accuracy. Our experiments show that the GPU-based implementation is the best implementation as it achieves performance 72.5X faster than the sequential implementation, whereas the best performance achieved by the POSIX threads and the SIMD techniques are 2X and 18.2X faster than the sequential implementation, respectively. |
Year | DOI | Venue |
|---|---|---|
2019 | 10.1007/s11042-017-5092-0 | Multimedia Tools and Applications |
Keywords | Field | DocType |
Bioinformatics, Global alignment, Needleman-Wunsch, POSIX threads, SIMD (Single Instruction Multiple Data), Graphics Processing Unit (GPU) | Dynamic programming,Computer science,Parallel computing,Vectorization (mathematics),SIMD,POSIX Threads,Implementation,Needleman–Wunsch algorithm,Software,POSIX | Journal |
Volume | Issue | ISSN |
78.0 | 4 | 1573-7721 |
Citations | PageRank | References |
14 | 0.51 | 10 |
Authors | ||
5 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Yaser Jararweh | 1 | 968 | 88.95 |
| Mahmoud Al-Ayyoub | 2 | 730 | 63.41 |
| Maged Fakirah | 3 | 14 | 0.51 |
| Luay Alawneh | 4 | 70 | 9.18 |
| B. B. Gupta | 5 | 518 | 46.49 |