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Protein database search of hybrid alignment algorithm based on GPU parallel acceleration

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Abstract

In biological research, alignment of protein sequences by computer is often needed to find similarities between them. Although results can be computed in a reasonable time for alignment of two sequences, it is still very central processing unit (CPU) time-consuming when solving massive sequences alignment problems such as protein database search. In this paper, an optimized protein database search method is presented and tested with Swiss-Prot database on graphic processing unit (GPU) devices, and further, the power of CPU multi-threaded computing is also involved to realize a GPU-based heterogeneous parallelism. In our proposed method, a hybrid alignment approach is implemented by combining Smith–Waterman local alignment algorithm with Needleman–Wunsch global alignment algorithm, and parallel database search is realized with compute unified device architecture (CUDA) parallel computing framework. In the experiment, the algorithm is tested on a lower-end and a higher-end personal computers equipped with GeForce GTX 750 Ti and GeForce GTX 1070 graphics cards, respectively. The results show that the parallel method proposed in this paper can achieve a speedup up to 138.86 times over the serial counterpart, improving efficiency and convenience of protein database search significantly.

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Acknowledgements

The authors would like to thank all the reviewers for their precious comments. This paper is supported by the Shandong Provincial Natural Science Foundation, China (Grant No. ZR2015CL020).

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Authors and Affiliations

  1. Equipment Division, Weifang Medical University, Weifang, 261053, Shandong, China

    Wei Zhou

  2. School of Bioscience and Technology, Weifang Medical University, Weifang, 261053, Shandong, China

    Zhanxiu Cai & Bo Lian

  3. Computer Staff Room, Weifang Medical University, Weifang, 261053, Shandong, China

    Jincai Wang

  4. School of Clinical Medicine, Weifang Medical University, Weifang, 261053, Shandong, China

    Jianping Ma

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  1. Wei Zhou
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  2. Zhanxiu Cai
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  3. Bo Lian
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  4. Jincai Wang
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  5. Jianping Ma
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Correspondence to Wei Zhou.

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Zhou, W., Cai, Z., Lian, B. et al. Protein database search of hybrid alignment algorithm based on GPU parallel acceleration. J Supercomput 73, 4517–4534 (2017). https://doi.org/10.1007/s11227-017-2030-x

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  • DOI: https://doi.org/10.1007/s11227-017-2030-x

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