Serial and parallel implementation of Needleman-Wunsch algorithm

(1) * Yun Sup Lee Mail (College of Computer Studies, De La Salle University, Philippines)
(2) Yu Sin Kim Mail (College of Computer Studies, De La Salle University, Philippines)
(3) Roger Luis Uy Mail (College of Computer Studies, De La Salle University, Philippines)
*corresponding author


Needleman-Wunsch dynamic programming algorithm measures the similarity of the pairwise sequence and finds the optimal pair given the number of sequences. The task becomes nontrivial as the number of sequences to compare or the length of sequences increases. This research aims to parallelize the computation involved in the algorithm to speed up the performance using CUDA. However, there is a data dependency issue due to the property of a dynamic programming algorithm. As a solution, this research introduces the heterogeneous anti-diagonal approach, which benefits from the interaction between the serial implementation on CPU and the parallel implementation on GPU. We then measure and compare the computation time between the proposed approach and a straightforward serial approach that uses CPU only. Measurements of computation times are performed under the same experimental setup and using various pairwise sequences at different lengths. The experiment showed that the proposed approach outperforms the serial method in terms of computation time by approximately three times. Moreover, the computation time of the proposed heterogeneous anti-diagonal approach increases gradually despite the big increments in sequence length, whereas the computation time of the serial approach grows rapidly.


Bioinformatics; Global alignment; Needleman-wunsch; GPU; CUDA



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