11541

Hybrid Framework for pairwise DNA Sequence Alignment Using the CUDA compatible GPU

H. Khaled, R. El Gohary, N.L. Badr, H. M. Faheem
Faculty of Computer & Information Science, Ain Shams University, Cairo, Egypt
The 2013 International Conference on Bioinformatics and Computational Biology (BIOCOMP’13), 2013

@article{khaled2013hybrid,

   title={Hybrid Framework for pairwise DNA Sequence Alignment Using the CUDA compatible GPU},

   author={Khaled, H and El Gohary, R and Badr, NL and Faheem, HM},

   journal={Proceeding of the BIOCO P},

   volume={3},

   year={2013}

}

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This paper provides a novel framework for accelerating the solution of the pairwise DNA sequence alignment problem using CUDA parallel paradigm available on the NVIDIA GPU. The main idea is to implement a new algorithm that assigns different nucleotide weights using GPU architectures then merge the subsequences of match using CPU to get the optimum local alignment. The paper describes both the algorithm and the implementation of it using both the GPU and CPU to constitute a hybrid model for solving DNA sequence alignment problem on DNA molecules. Experimental results demonstrate a considerable reduction in run time relative to traditional Smith-Waterman implementation on traditional processors.
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