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GPU technology as a platform for accelerating local complexity analysis of protein sequences.

Agathoklis Papadopoulos, Ioannis Kirmitzoglou, Vasilis J Promponas

    Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference
    |October 11, 2013
    PubMed
    Summary
    This summary is machine-generated.

    We developed GPU_CAST, a CUDA-enabled version of CAST software, to accelerate the identification of low-complexity regions (LCRs) in protein sequences. This GPU-based approach achieves significant speedups, enhancing bioinformatics analysis.

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    Area of Science:

    • Bioinformatics
    • Computational Biology
    • High-Performance Computing

    Background:

    • Bioinformatics tools like CAST are crucial for analyzing protein sequences.
    • Identifying low-complexity regions (LCRs) in proteins is computationally intensive.
    • General-Purpose Graphics Unit (GPGPU) programming offers potential for accelerating bioinformatics algorithms.

    Purpose of the Study:

    • To develop a GPU-accelerated version of the CAST algorithm for masking LCRs in protein sequences.
    • To leverage the GPGPU programming paradigm and CUDA for enhanced computational efficiency.
    • To evaluate the performance of the GPU-based implementation against existing multi-threaded versions.

    Main Methods:

    • Implemented a CUDA-enabled version of the CAST software (GPU_CAST).
    • Utilized NVIDIA CUDA libraries and the GPGPU programming paradigm.
    • Executed calculations on GPU cards for parallel processing.
    • Compared GPU_CAST performance against a multi-threaded, multi-core optimized CAST version.

    Main Results:

    • Achieved significant speedups of 5x-10x for large protein sequence datasets.
    • Demonstrated the effectiveness of GPGPU in accelerating sequence analysis algorithms.
    • Validated the performance gains of the GPU-based implementation.

    Conclusions:

    • GPU_CAST provides a substantial performance improvement for LCR masking in protein sequences.
    • GPGPU programming is a viable strategy for accelerating computationally demanding bioinformatics tasks.
    • The developed GPU_CAST software enhances the efficiency of protein sequence analysis in bioinformatics.