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Parallelization of Weighted Sequence Comparison by using EBWT

Binay Kumar Pandey, Shashank Srikant, Dr. Rajdeep Niyogi, Dr. Ankush Mittal
Electronics and Computer Engineering Department, Indian Institute of Technology, Roorkee, India
arXiv:1011.0597 [cs.DC] (2 Nov 2010)

@article{pandey2010parallelization,

   title={Parallelization of Weighted Sequence Comparison by using EBWT},

   author={Pandey, B.K. and Srikant, S. and Niyogi, D. and Mittal, D. and others},

   journal={Arxiv preprint arXiv:1011.0597},

   year={2010}

}

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The Extended Burrows Wheeler transform (EBWT) helps to find the distance between two sequences. Implementation of an existing algorithm takes considerable amount of time for small size sequences. In this paper, we give a parallel implementation of this algorithm using NVIDIA Compute Unified Device Architecture (CUDA). We have obtained, on an average, a 2X improvement in the performance.
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