International Journal of Computer Applications
Foundation of Computer Science (FCS), NY, USA
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Volume 63 - Issue 1 |
Published: February 2013 |
Authors: Muralidhara B L |
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Muralidhara B L . Staircase Method: A Novel Method for Parallelizing S-W Algorithm. International Journal of Computer Applications. 63, 1 (February 2013), 1-7. DOI=10.5120/10427-5096
@article{ 10.5120/10427-5096, author = { Muralidhara B L }, title = { Staircase Method: A Novel Method for Parallelizing S-W Algorithm }, journal = { International Journal of Computer Applications }, year = { 2013 }, volume = { 63 }, number = { 1 }, pages = { 1-7 }, doi = { 10.5120/10427-5096 }, publisher = { Foundation of Computer Science (FCS), NY, USA } }
%0 Journal Article %D 2013 %A Muralidhara B L %T Staircase Method: A Novel Method for Parallelizing S-W Algorithm%T %J International Journal of Computer Applications %V 63 %N 1 %P 1-7 %R 10.5120/10427-5096 %I Foundation of Computer Science (FCS), NY, USA
Sequence comparison is a basic operation in DNA sequencing projects, and most of sequence comparison methods are based on heuristics, which are fast but not sensitive. The Dynamic Programming Algorithm, Smith-Waterman, obtains the best alignment, but at the expense of computational time. Unfortunately, the inefficiency in the performance of the Smith-Waterman algorithm limits its applications in the real world. A possible way out of this is to use parallelization methods for decreasing the time taken to execute the algorithm. In this paper, we present a two master method and a novel parallel technique called staircase method to improve the performance of the Smith-Waterman algorithm.