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Accelerating Search of Protein Sequence Databases using CUDA-Enabled GPU

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Database Systems for Advanced Applications (DASFAA 2015)

Part of the book series: Lecture Notes in Computer Science ((LNISA,volume 9049))

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Abstract

Searching databases of protein sequences for those proteins that match patterns represented as profile HMMs is a widely performed bioinformatics task. The standard tool for the task is HMMER version 3 from Sean Eddy. HMMER3 achieved significant improvements in performance over version 2 through the introduction of a heuristic filter called the Multiple Segment Viterbi algorithm (MSV) and the use of native SIMD instruction set on modern CPUs. Our objective was to further improve performance by using a general-purpose graphical processing unit (GPU) and the CUDA software environment from Nvidia.

An execution profile of HMMER3 identifies the MSV filter as a code hotspot that consumes over 75% of the total execution time. We applied a number of well-known optimization strategies for coding GPUs in order to implement a CUDA version of the MSV filter.

The results show that our implementation achieved 1.8x speedup over the single-threaded HMMER3 CPU SSE2 implementation on average. The experiments used a modern Kepler architecture GPU from Nvidia that has 768 cores running at 811 Mhz and an Intel Core i7-3960X 3.3GHz CPU overclocked at 4.6GHz.

For HMMER2 there was a significant speed-up of an order of magnitude obtained by implementations using GPUs. Such gains seem out of reach for HMMER3.

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Author information

Authors and Affiliations

  1. Department of Computer Science and Software Engineering, Concordia University, Montreal, Canada

    Lin Cheng & Greg Butler

Authors
  1. Lin Cheng
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  2. Greg Butler
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Correspondence to Greg Butler .

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Editors and Affiliations

  1. Universität München, München, Germany

    Matthias Renz

  2. University of Southern California, Los Angeles, USA

    Cyrus Shahabi

  3. University of Queensland, Brisbane, Australia

    Xiaofang Zhou

  4. Monash University, Clayton, Australia

    Muhammad Aamir Cheema

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Cheng, L., Butler, G. (2015). Accelerating Search of Protein Sequence Databases using CUDA-Enabled GPU. In: Renz, M., Shahabi, C., Zhou, X., Cheema, M. (eds) Database Systems for Advanced Applications. DASFAA 2015. Lecture Notes in Computer Science(), vol 9049. Springer, Cham. https://doi.org/10.1007/978-3-319-18120-2_17

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  • DOI: https://doi.org/10.1007/978-3-319-18120-2_17

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-18119-6

  • Online ISBN: 978-3-319-18120-2

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