Design and Implementation of the Smith-Waterman Algorithm on the CUDA-Compatible GPU

8th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2008

Volumn , Issue , 2008, Pages

  Munekawa, Yuma ^a   Ino, Fumihiko ^a   Hagihara, Kenichi ^a  

^a OSAKA UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; COMPUTE UNIFIED DEVICE ARCHITECTURES; DATA REUSE; GRAPHICS PROCESSING UNIT; NUMBER OF DATUM; OFF-CHIP MEMORIES; ON CHIPS; PEAK PERFORMANCE; PROCESSING ELEMENTS; SHARED MEMORIES; SMITH-WATERMAN ALGORITHM;

AMINES; AMINO ACIDS; BIOINFORMATICS; IMAGE CODING; MULTIPROCESSING SYSTEMS; ORGANIC ACIDS;

DATA REDUCTION;

EID: 67549093800     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBE.2008.4696721     Document Type: Conference Paper

References (15)

1. T. F. Smith and M. S. Waterman, "Identification of common molecular subsequences," J. Molecular Biology, vol. 147, pp. 195-197, 1981.
2. A. Bairoch and R. Apweiler, "The SWISS-PROT protein sequence data bank and its supplement TrEMBL," Nucleic Acids Research, vol. 25, no. 1, pp. 31-36, Jan. 1997.
3. D. A. Benson, I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, B. A. Rapp, and D. L. Wheeler, "GenBank," Nucleic Acids Research, vol. 28, no. 1, pp. 15-18, Jan. 2000.
4. S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, "Basic local alignment search tool," J. Molecular Biology, vol. 215, no. 3, pp. 403-410, Oct. 1990.
5. W. R. Pearson, "Searching protein sequence libraries: Comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms," Genomics, vol. 11, no. 3, pp. 635-650, Nov. 1991.
6. S. A. Manavski and G. Valle, "CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment," BMC Bioinformatics, vol. 9, no. S10, Mar. 2008, 9 pages.
7. J. D. Owens, M. Houston, D. Luebke, S. Green, J. E. Stone, and J. C. Phillips, "GPU computing," Proceedings of the IEEE, vol. 96, no. 5, pp. 879-899, May 2008.
8. nVIDIA Corporation, "CUDA Programming Guide Version 1.1," Nov. 2007. [Online]. Available: http://developer.nvidia.com/cuda/
9. W. Liu, B. Schmidt, G. Voss, and W. Muller-Wittig, "Streaming algorithms for biological sequence alignment on GPUs," IEEE Trans. Parallel and Distributed Systems, vol. 18, no. 9, pp. 1270-1281, Sep. 2007.
10. D. Shreiner, M. Woo, J. Neider, and T. Davis, OpenGL Programming Guide, 5th ed. Reading, MA: Addison-Wesley, Aug. 2005.
11. M. C. Schatz, C. Trapnell, A. L. Delcher, and A. Varshney, "High- throughput sequence alignment using graphics processing units," BMC Bioinformatics, vol. 8, no. 474, Dec. 2007, 10 pages.
12. M. Farrar, "Striped Smith-Waterman speeds database searches six times over other SIMD implementations," Bioinformatics, vol. 23, no. 2, pp. 156-161, Jan. 2007.
13. P. Zhang, G. Tan, and G. R. Gao, "Implementation of the Smith- Waterman algorithm on a reconfigurable supercomputing platform," in Proc. 1st Workshop High-performance reconfigurable computing technology and applications (HPRCTA'06), Nov. 2007, pp. 39-48.
14. I. T. 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, no. 185, Jun. 2007, 7 pages.
15. W. R. Mark, R. S. Glanville, K. Akeley, and M. J. Kilgard, "Cg: A system for programming graphics hardware in a C-like language," ACM Trans. Graphics, vol. 22, no. 3, pp. 896-897, Jul. 2003.