CUDASW++2.0: Enhanced Smith-Waterman protein database search on CUDA-enabled GPUs based on SIMT and virtualized SIMD abstractions

BMC Research Notes

Volumn 3, Issue , 2010, Pages

  Liu, Yongchao ^a   Schmidt, Bertil ^a   Maskell, Douglas L ^a  

^a NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77951106340     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-3-93     Document Type: Article

References (25)

1. Identification of common molecular subsequences. T Smith M Waterman, J Molecular Biology 1981 147 195 197 10.1016/0022-2836(81)90087-5
2. An improved algorithm for matching biological sequences. O Gotoh, J Mol Biol 1982 162 707 708 10.1016/0022-2836(82)90398-9
3. Improved tools for biological sequence comparison. WR Pearson DJ Lipman, Proc Nat Acad Sci USA 1988 85 8 2444 2448 10.1073/pnas.85.8.2444 3162770
4. Basic local alignment search tool. SF Altschul W Gish W Miller EW Myers DJ Lipman, J Mol Biol 1990 215 3 403 410 2231712 (Pubitemid 20364473)
5. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. SF Altschul TL Madden AA Schaffer J Zhang Z Zhang W Miller DJ Lipman, Nucleic Acids Res 1997 25 17 3389 3402 10.1093/nar/25.17.3389 9254694 (Pubitemid 27359211)
6. Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW. T Oliver B Schmidt D Nathan R Clemens D Maskell, Bioinformatics 2005 21 16 3431 3432 10.1093/bioinformatics/bti508 15919726 (Pubitemid 41222452)
7. Reconfigurable architectures for bio-sequence database scanning on FPGAs. T Oliver B Schmidt DL Maskell, IEEE Trans Circuit Syst II 2005 52 851 855 10.1109/TCSII.2005.853340 (Pubitemid 43056340)
8. 160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA). TI Li W Shum K Truong, BMC Bioinformatics 2007 8 85 10.1186/1471-2105-8-85
9. Using video-oriented instructions to speed up sequence comparison. A Wozniak, Comput Appl Biosci 1997 13 2 145 150 9146961 (Pubitemid 27189999)
10. Six-fold speedup of Smith-Waterman sequence database searches using parallel processing on common microprocessors. T Rognes E Seeberg, Bioinformatics 2000 16 8 699 706 10.1093/bioinformatics/16.8.699 11099256
11. Striped Smith-Waterman speeds database searches six times over other SIMD implementations. M Farrar, Bioinformatics 2007 23 2 156 161 10.1093/bioinformatics/btl582 17110365 (Pubitemid 46189604)
12. Optimizing Smith-Waterman for the Cell broadband engine. MS Farrar, http://farrar.michael.googlepages.com/SW-CellBE.pdf 9130873
13. SWPS3 - fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and ×86/SSE2. A Szalkowski C Ledergerber P Krahenbuhl C Dessimoz, BMC Research Notes 2008 1 107 10.1186/1756-0500-1-107 18959793
14. CBESW: sequence alignment on Playstation 3. A Wirawan CK Kwoh NT Hieu B Schmidt, BMC Bioinformatics 2008 9 377 10.1186/1471-2105-9-377 18798993
15. Streaming algorithms for biological sequence alignment on GPUs. W Liu B Schmidt G Voss W Muller-Wittig, IEEE Transactions on Parallel and Distributed Systems 2007 18 9 1270 1281 10.1109/TPDS.2007.1059 (Pubitemid 47322988)
16. CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment. SA Manavski G Valle, BMC Bioinformatics 2008 9 Suppl 2 10 10.1186/1471-2105-9-S2-S10 18387198
17. CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units. Y Liu DL Maskell B Schmidt, BMC Research Notes 2009 2 73 10.1186/1756-0500-2-73 19416548
18. Scalable parallel programming with CUDA. J Nickolls I Buck M Garland K Skadron, ACM Queue 2008 6 2 40 53 10.1145/1365490.1365500
19. NVIDIA Tesla: A unified graphics and computing architecture. E Lindholm J Nickolls S Oberman J Montrym, IEEE Micro 2008 28 2 39 55 10.1109/MM.2008.31 (Pubitemid 351796170)
20. NVIDIA CUDA programming guide version 2.0. http://developer.download. nvidia.com/compute/cuda/2-0/docs/NVIDIA-CUDA-Programming-Guide-2.0.pdf
21. CLUSTALW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. JD Thompson DG Higgins TJ Gibson, Nucleic Acids Res 1994 22 4673 4680 10.1093/nar/22.22.4673 7984417
22. Clustal W and Clustal X version 2.0. MA Larkin G Blackshields NP Brown R Chenna PA McGettigan H McWilliam F Valentin IM Wallace1 A Wilm R Lopez JD Thompson JD Gibson DG Higgins, Bioinformatics Applications Note 2007 23 21 2947 2948
23. Significance of Z-value statistics of Smith-Waterman scores for protein alignments. JP Comet JC Aude E Glémet JL Risler A Hénaut PP Slonimski JJ Codani, Computers & Chemistry 1999 23 3-4 317 331
24. Fundamentals of massive automatic pairwise alignments of protein sequences: theoretical significance of Z-value statistics. O Bastien JC Aude S Roy E Maréchal, Bioinformatics 2004 20 4 534 537 10.1093/bioinformatics/ btg440 14990449
25. A Screening Method for Z-Value Assessment Based on the Normalized Edit Distance. G Peris A Marzal, Lecture Notes in Computer Science 2009 5518 1154 1161 full-text