Name
Title | ||
|---|---|---|
Accelerating the Smith-Waterman algorithm with interpair pruning and band optimization for the all-pairs comparison of base sequences |
Abstract | ||
|---|---|---|
The Smith-Waterman algorithm is known to be a more sensitive approach than heuristic algorithms for local sequence alignment algorithms. Despite its sensitivity, a greater time complexity associated with the Smith-Waterman algorithm prevents its application to the all-pairs comparisons of base sequences, which aids in the construction of accurate phylogenetic trees. The aim of this study is to achieve greater acceleration using the Smith-Waterman algorithm (by realizing interpair block pruning and band optimization) compared with that achieved using a previous method that performs intrapair block pruning on graphics processing units (GPUs). |
Year | DOI | Venue |
|---|---|---|
2015 | 10.1186/s12859-015-0744-4 | BMC Bioinformatics |
Keywords | Field | DocType |
Local alignment, Smith-Waterman algorithm, All-pairs comparison, Pruning | Sequence alignment,Graphics,Heuristic,Computer science,Algorithm,Acceleration,Smith–Waterman algorithm,Bioinformatics,Time complexity,Pruning | Journal |
Volume | Issue | ISSN |
16 | 1 | 1471-2105 |
Citations | PageRank | References |
2 | 0.40 | 19 |
Authors | ||
3 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Daiki Okada | 1 | 2 | 0.40 |
| Fumihiko Ino | 2 | 317 | 38.63 |
| Kenichi Hagihara | 3 | 528 | 56.94 |