About this Journal Submit a Manuscript Table of Contents
BioMed Research International
Volume 2013 (2013), Article ID 721738, 8 pages
http://dx.doi.org/10.1155/2013/721738
Research Article

GPU-Based Cloud Service for Smith-Waterman Algorithm Using Frequency Distance Filtration Scheme

1Department of Computer Science and Information Engineering, Chang Gung University, No. 259 Sanmin Road, Guishan, Taoyuan 33302, Taiwan
2Department of Computer Science & Communication Engineering, Providence University, No. 200 Section 7, Taiwan Boulevard, Shalu, Taichung 43301, Taiwan

Received 7 December 2012; Accepted 13 March 2013

Academic Editor: Ching-Hsien Hsu

Copyright © 2013 Sheng-Ta Lee et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. T. F. Smith and M. S. Waterman, “Identification of common molecular subsequences,” Journal of Molecular Biology, vol. 147, no. 1, pp. 195–197, 1981. View at Scopus
  2. O. Gotoh, “An improved algorithm for matching biological sequences,” Journal of Molecular Biology, vol. 162, no. 3, pp. 705–708, 1982.
  3. D. W. Mount, Sequence and Genome Analysis, Cold Spring Harbor Laboratory Press, 2004.
  4. W. R. Pearson and D. J. Lipman, “Improved tools for biological sequence comparison,” Proceedings of the National Academy of Sciences of the United States of America, vol. 85, no. 8, pp. 2444–2448, 1988.
  5. S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, “Basic local alignment search tool,” Journal of Molecular Biology, vol. 215, no. 3, pp. 403–410, 1990. View at Publisher · View at Google Scholar · View at Scopus
  6. S. F. Altschul, T. L. Madden, A. A. Schäffer et al., “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs,” Nucleic Acids Research, vol. 25, no. 17, pp. 3389–3402, 1997. View at Publisher · View at Google Scholar · View at Scopus
  7. T. Oliver, B. Schmidt, D. Nathan, R. Clemens, and D. L. Maskell, “Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW,” Bioinformatics, vol. 21, no. 16, pp. 3431–3432, 2005. View at Publisher · View at Google Scholar · View at Scopus
  8. T. Oliver, B. Schmidt, and D. L. Maskell, “Reconfigurable architectures for bio-sequence database scanning on FPGAs,” IEEE Transactions on Circuits and Systems II, vol. 52, pp. 851–855, 2005.
  9. I. T. S. Li, W. Shum, and K. Truong, “160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA),” BMC Bioinformatics, vol. 8, article 185, 2007. View at Publisher · View at Google Scholar · View at Scopus
  10. A. Szalkowski, C. Ledergerber, P. Krahenbuhl, and C. Dessimoz, “SWPS3—fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and x86/SSE2,” BMC Research Notes, vol. 1, p. 107, 2008.
  11. M. S. Farrar, “Optimizing Smith-Waterman for the Cell Broadband Engine,” http://farrar.michael.googlepages.com/SW-CellBE.pdf.
  12. A. Wirawan, C. K. Kwoh, N. T. Hieu, and B. Schmidt, “CBESW: sequence alignment on the playstation 3,” BMC Bioinformatics, vol. 9, article 377, 2008. View at Publisher · View at Google Scholar · View at Scopus
  13. Y. Liu, W. Huang, J. Johnson, and S. H. Vaidya, “GPU accelerated smith–waterman,” in Proceedings of the Computational Science (ICCS '06), vol. 3994 of Lecture Notes in Computer Science, Part 4, pp. 188–195.
  14. NVIDIA GPU Computing Documentations, http://docs.nvidia.com/cuda/index.html.
  15. W. Liu, B. Schmidt, G. Voss, and W. Müller-Wittig, “Streaming algorithms for biological sequence alignment on GPUs,” IEEE Transactions on Parallel and Distributed Systems, vol. 18, no. 9, pp. 1270–1281, 2007. View at Publisher · View at Google Scholar · View at Scopus
  16. S. A. Manavski and G. Valle, “CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment,” BMC Bioinformatics, vol. 9, supplement 2, article S10, 2008. View at Publisher · View at Google Scholar · View at Scopus
  17. Y. Liu, D. L. Maskell, and B. Schmidt, “CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units,” BMC Research Notes, vol. 2, article 73, 2009. View at Publisher · View at Google Scholar · View at Scopus
  18. Y. Liu, B. Schmidt, and D. L. Maskell, “CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions,” BMC Research Notes, vol. 3, article 93, 2010. View at Publisher · View at Google Scholar · View at Scopus
  19. T. Kahveci, V. Ljosa, and A. K. Singh, “Speeding up whole-genome alignment by indexing frequency vectors,” Bioinformatics, vol. 20, no. 13, pp. 2122–2134, 2004. View at Publisher · View at Google Scholar · View at Scopus
  20. S. Henikoff and J. G. Henikoff, “Amino acid substitution matrices from protein blocks,” Proceedings of the National Academy of Sciences of the United States of America, vol. 89, no. 22, pp. 10915–10919, 1992. View at Publisher · View at Google Scholar · View at Scopus
  21. M. O. Dayhoff, R. M. Schwartz, B. C. Orcutt, et al., “A model of evolutionary change in proteins,” in Atlas of Protein Sequence and Structure, M. O. Dayhoff, Ed., National Biomedical Research Foundation, 1978.
  22. A. Wozniak, “Using video-oriented instructions to speed up sequence comparison,” Computer Applications in the Biosciences, vol. 13, no. 2, pp. 145–150, 1997. View at Scopus
  23. T. Rognes and E. Seeberg, “Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors,” Bioinformatics, vol. 16, no. 8, pp. 699–706, 2000. View at Scopus
  24. M. Farrar, “Striped Smith-Waterman speeds database searches six times over other SIMD implementations,” Bioinformatics, vol. 23, no. 2, pp. 156–161, 2007. View at Publisher · View at Google Scholar · View at Scopus
  25. B. Alpern, L. Carter, and K. S. Gatlin, “Microparallelism and high-performance protein matching,” in Proceedings of the ACM/IEEE Supercomputing Conference, pp. 536–551, December 1995. View at Scopus
  26. W. R. Rudnicki, A. Jankowski, A. Modzelewski, A. Piotrowski, and A. Zadrozny, “The new SIMD implementation of the smith-waterman algorithm on cell microprocessor,” Fundamenta Informaticae, vol. 96, no. 1-2, pp. 181–194, 2009. View at Publisher · View at Google Scholar · View at Scopus
  27. Y. Liu, B. Schmidt, and D. L. Maskell, “MSA-CUDA: multiple sequence alignment on graphics processing units with CUDA,” in Proceedings of the 20th IEEE International Conference on Application-Specific Systems, Architectures and Processors (ASAP '09), pp. 121–128, July 2009. View at Publisher · View at Google Scholar · View at Scopus
  28. A. Khajeh-Saeed, S. Poole, and J. B. Perot, “Acceleration of the Smith-Waterman algorithm using single and multiple graphics processors,” Journal of Computational Physics, vol. 229, no. 11, pp. 4247–4258, 2010. View at Publisher · View at Google Scholar · View at Scopus