Optimizing Smith-Waterman algoritm on Graphics Processing Unit

ICCTD 2010 - 2010 2nd International Conference on Computer Technology and Development, Proceedings

Volumn , Issue , 2010, Pages 650-654

  Khalafallah, Ayman ^a   Elbabb, Hosain Fath ^a   Mahmoud, Omar ^a   Elshamy, Ahmed ^a  

^a Alexandria University The Faculty Of Engineering   (Egypt)

Author keywords

GPU; OpenCL; Parallel; Smith Waterman

Indexed keywords

BIOLOGICAL DATABASE; GPU; GRAPHICS PROCESSING UNIT; LOCAL SEQUENCES; OPEN STANDARDS; OPENCL; PARALLEL; PARALLEL IMPLEMENTATIONS; QUADRATIC TIME; SMITH-WATERMAN; SMITH-WATERMAN ALGORITHM;

ALGORITHMS; BIOINFORMATICS; PARALLEL ARCHITECTURES; PROGRAM PROCESSORS; SEARCH ENGINES;

COMPUTER GRAPHICS EQUIPMENT;

EID: 78650601096     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ICCTD.2010.5645976     Document Type: Conference Paper

References (17)

1. Smith T, Waterman M "Identification of Common Molecular Subsequences," in J Molecular Biology 1981, 147:195-197.
2. Yongchao Liu, Douglas L Maskell, Bertil Schmidt "CUDASW++: optimizing Smith-Waterman sequence database searches for CUDAenabled graphics processing units," in BMC Bioiriformatics 2009, 9(Suppl 2) S 10.
3. Yongchao Liu, Douglas L Maskell, Bertil Schmidt "CUDASW++2.0: enhanced Smith-Waterman protein database search on CUDAenabled GPUs based on SIMT and virtualized SIMD abstractions," in BMC Research Notes 2010, 3:93.
4. Pearson WR, Lipman DJ "Improved tools for biological sequence comparison," in Proc Nat A cad Sci USA 1988, 85(8):2444-2448.
5. Altschul SF, Gish W, Miller W, Myers EW, Lipman OJ "Basical local alignment search tool," in J Mol Biol 1990, 215(3):403-410.
6. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman OJ "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs," in Nucleic Acids Res 1997, 25(17):3389-3402.
7. Oliver T, Schmidt B, Nathan D, Clemens R, Maskell D "Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW," in Bioiriformatics 2005, 21 (16):3431-3432.
8. Oliver T, Schmidt B, Maskell DL. "Reconfigurable architectures for bio-sequence database scanning on FPGAs," in IEEE Trans. Circuit Syst. II 2005, 52:851-855. (Pubitemid 43056340)
9. Li n, Shum W, Truong K "160-fold acceleration of the SmithWaterman algorithm using a field programmable gate array (FPGA)," in BMC Bioiriformatics 2007, 8:I85.
10. Farrar M "Striped Smith-Waterman speeds database searches six times over other SIMD implementations," in Bioinformatics 2007, 23(2):156-161.
11. Farrar MS: "Optimizing Smith-Waterman for the Cell Broadband Engine ".
12. Szalkowski A, Ledergerber C, Krahenbuhl P, Dessimoz C "SWPS3- fast multi-threaded vectorized SmithWaterman for IBM CelllB.E. and x86/SSE2," in BMC Research Notes 2008, 1: 107.
13. Wirawan A, Kwoh CK, Hieu NT, Schmidt B: CBESW'Sequence Alignment on Playstation 3," in BMC Bioiriformatics 2008, 9:377.
14. Liu W, Schmidt B, Voss G, Muller-Wittig W'Streaming algorithms for biological sequence alignment on GPUs," in IEEE Transactions on Parallel and Distributed Systems 2007, 18(9): 1270-1281.
15. Manavski SA, Valle G "CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment," in BMC Bioiriformatics 2008, 9(Suppl 2):S10.
16. Wozniak A "Using video-oriented instructions to speed up sequence comparison," in ComputAppl Biosci 1997, 13(2):145-150.
17. Rognes T, Seeberg E " Six-fold speedup of Smith-Waterman sequence database searches using parallel processing on common microprocessors," in Bioiriformatics 2000, 16(8):699-706.