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CLUS_GPU-BLASTP: accelerated protein sequence alignment using GPU-enabled cluster

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Abstract

Basic Local Alignment Search Tool (BLAST) is one of the most frequently used algorithms for bioinformatics applications. In this paper, an accelerated implementation of protein BLAST, i.e., CLUS_GPU-BLASTP for multiple query sequence processing in parallel, on graphical processing unit (GPU)-enabled high-performance cluster is proposed. The experimental setup consisted of a high-performance GPU-enabled cluster. Each compute node of the cluster consisted of two hex-core Intel, Xeon 2.93 GHz processors with 50 GB RAM and 12 MB cache. Each compute node was also equipped with a NVIDIA M2050 GPU. In comparison with the famous GPU-BLAST, our BLAST implementation is 2.1 times faster on single compute node. On a cluster of 12 compute nodes, our implementation gave a speedup of 13.2X. In comparison with standard single-threaded NCBI-BLAST, our implementation achieves a speedup ranging from 7.4X to 8.2X.

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Acknowledgements

The authors express deep gratitude to the Dean, Research, Innovation and Consultancy Department of I.K.G. Punjab Technical University, Kapurthala, for giving them the opportunity to carry on this research work.

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Authors and Affiliations

  1. I.K.G. Punjab Technical University, Kapurthala, Punjab, India

    Sita Rani

  2. School of Electrical Engineering and Information Technology, Punjab Agricultural University, Ludhiana, Punjab, India

    O. P. Gupta

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  1. Sita Rani
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  2. O. P. Gupta
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Correspondence to Sita Rani.

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Rani, S., Gupta, O.P. CLUS_GPU-BLASTP: accelerated protein sequence alignment using GPU-enabled cluster. J Supercomput 73, 4580–4595 (2017). https://doi.org/10.1007/s11227-017-2036-4

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  • DOI: https://doi.org/10.1007/s11227-017-2036-4

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