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Optimizing Smith-Waterman algorithm on Graphics Processing Unit

A. Khalafallah, H.F. Elbabb, O. Mahmoud, A. Elshamy
Dept. of Comput. Eng. & Syst., Alexandria Univ., Alexandria, Egypt
2nd International Conference on Computer Technology and Development (ICCTD), 2010

@conference{khalafallah2010optimizing,

   title={Optimizing Smith-Waterman algorithm on Graphics Processing Unit},

   author={Khalafallah, A. and Elbabb, H.F. and Mahmoud, O. and Elshamy, A.},

   booktitle={Computer Technology and Development (ICCTD), 2010 2nd International Conference on},

   pages={650–654},

   organization={IEEE}

}

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Local Sequence alignment is an important task for bioinformatics. The most widely used algorithm is Smith-Waterman has a quadratic time complexity which is time consuming especially in large biological database search. Many attempts were made to accelerate Smith-Waterman using parallel architecture. In this paper a parallel implementation of Smith Waterman algorithm will be presented. This implementation will run on Graphics Processing Unit using an open standard (OpenCL) by carefully exploiting features of the graphics processing unit, this implementation will be more than two times faster than the other parallel implementation on the Graphics Processing Unit.
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