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International Conference on Parallel Processing and Applied Mathematics

PPAM 2013: Parallel Processing and Applied Mathematics pp 247–257Cite as

Faster GPU-Accelerated Smith-Waterman Algorithm with Alignment Backtracking for Short DNA Sequences

Part of the Lecture Notes in Computer Science book series (LNTCS,volume 8385)

Abstract

In this paper, we present a GPU-accelerated Smith-Waterman (SW) algorithm with Alignment Backtracking, called GSWAB, for short DNA sequences. This algorithm performs all-to-all pairwise alignments and retrieves optimal local alignments on CUDA-enabled GPUs. To facilitate fast alignment backtracking, we have investigated a tile-based SW implementation using the CUDA programming model. This tiled computing pattern enables us to more deeply explore the powerful compute capability of GPUs. We have evaluated the performance of GSWAB on a Kepler-based GeForce GTX Titan graphics card. The results show that GSWAB can achieve a performance of up to 56.8 GCUPS on large-scale datasets. Furthermore, our algorithm yields a speedup of up to 53.4 and 10.9 over MSA-CUDA (the first stage) and gpu-pairAlign on the same hardware configurations.

Keywords

  • Smith-Waterman
  • Sequence alignment
  • Alignment backtracking
  • CUDA
  • GPU

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Authors and Affiliations

  1. Institut für Informatik, Johannes Gutenberg Universität Mainz, 55099, Mainz, Germany

    Yongchao Liu & Bertil Schmidt

Authors
  1. Yongchao Liu
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  2. Bertil Schmidt
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Correspondence to Yongchao Liu .

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Editors and Affiliations

  1. Institute of Computer and Information Science, Czestochowa University of Technology, Czestochowa, Poland

    Roman Wyrzykowski

  2. University of Tennessee, Department of Computer Science, Knoxville, Tennessee, USA

    Jack Dongarra

  3. Institute of Computer and Information Science, Czestochowa University of Technology, Czestochowa, Poland

    Konrad Karczewski

  4. Technical University of Denmark Informatics and Mathematical Modelling, Kongens Lyngby, Denmark

    Jerzy Waśniewski

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Liu, Y., Schmidt, B. (2014). Faster GPU-Accelerated Smith-Waterman Algorithm with Alignment Backtracking for Short DNA Sequences. In: Wyrzykowski, R., Dongarra, J., Karczewski, K., Waśniewski, J. (eds) Parallel Processing and Applied Mathematics. PPAM 2013. Lecture Notes in Computer Science(), vol 8385. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-55195-6_23

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  • DOI: https://doi.org/10.1007/978-3-642-55195-6_23

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