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Volumn 2, Issue , 2009, Pages

CUDASW++: Optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units

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EID: 74549205661     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-2-73     Document Type: Article
Times cited : (197)

References (20)
  • 1
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • 10.1016/0022-2836(81)90087-5
    • Identification of Common Molecular Subsequences. T Smith M Waterman, J Molecular Biology 1981 147 195 197 10.1016/0022-2836(81)90087-5
    • (1981) J Molecular Biology , vol.147 , pp. 195-197
    • Smith, T.1    Waterman, M.2
  • 2
    • 0020484488 scopus 로고
    • An improved algorithm for matching biological sequences
    • 10.1016/0022-2836(82)90398-9
    • An improved algorithm for matching biological sequences. O Gotoh, J Mol Biol 1982 162 707 708 10.1016/0022-2836(82)90398-9
    • (1982) J Mol Biol , vol.162 , pp. 707-708
    • Gotoh, O.1
  • 3
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • 3162770. 10.1073/pnas.85.8.2444
    • Improved tools for biological sequence comparison. WR Pearson DJ Lipman, Proc Nat Acad Sci USA 1988 85 8 2444 2448 3162770 10.1073/pnas.85.8.2444
    • (1988) Proc Nat Acad Sci USA , vol.85 , Issue.8 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 5
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
    • DOI 10.1093/nar/25.17.3389
    • 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 9254694 10.1093/nar/25.17.3389 (Pubitemid 27359211)
    • (1997) Nucleic Acids Research , vol.25 , Issue.17 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5    Miller, W.6    Lipman, D.J.7
  • 6
    • 24044471657 scopus 로고    scopus 로고
    • Using reconfigurable hardware to accelerate multiple sequence alignment with ClustalW
    • DOI 10.1093/bioinformatics/bti508
    • 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 15919726 10.1093/bioinformatics/bti508 (Pubitemid 41222452)
    • (2005) Bioinformatics , vol.21 , Issue.16 , pp. 3431-3432
    • Oliver, T.1    Schmidt, B.2    Nathan, D.3    Clemens, R.4    Maskell, D.5
  • 8
    • 34347225963 scopus 로고    scopus 로고
    • 160-fold acceleration of the Smith-Waterman algorithm using a field programmable gate array (FPGA)
    • 10.1186/1471-2105-8-85
    • 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
    • (2007) BMC Bioinformatics , vol.8 , pp. 985
    • Li, T.I.1    Shum, W.2    Truong, K.3
  • 9
    • 33846697176 scopus 로고    scopus 로고
    • Striped Smith-Waterman speeds database searches six times over other SIMD implementations
    • DOI 10.1093/bioinformatics/btl582
    • Striped Smith-Waterman speeds database searches six times over other SIMD implementations. M Farrar, Bioinformatics 2007 23 2 156 161 17110365 10.1093/bioinformatics/btl582 (Pubitemid 46189604)
    • (2007) Bioinformatics , vol.23 , Issue.2 , pp. 156-161
    • Farrar, M.1
  • 10
    • 77049114671 scopus 로고    scopus 로고
    • SWPS3 - Fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and x86/SSE2
    • 18959793. 10.1186/1756-0500-1-107
    • SWPS3 - fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and x86/SSE2. A Szalkowski C Ledergerber P Krahenbuhl C Dessimoz, BMC Research Notes 2008 1 107 18959793 10.1186/1756-0500-1-107
    • (2008) BMC Research Notes , vol.1 , pp. 107
    • Szalkowski, A.1    Ledergerber, C.2    Krahenbuhl, P.3    Dessimoz, C.4
  • 12
    • 53749090746 scopus 로고    scopus 로고
    • CBESW: Sequence alignment on playstation 3
    • 18798993. 10.1186/1471-2105-9-377
    • CBESW: Sequence Alignment on Playstation 3. A Wirawan CK Kwoh NT Hieu B Schmidt, BMC Bioinformatics 2008 9 377 18798993 10.1186/1471-2105-9-377
    • (2008) BMC Bioinformatics , vol.9 , pp. 377
    • Wirawan, A.1    Kwoh, C.K.2    Hieu, N.T.3    Schmidt, B.4
  • 13
    • 34548238659 scopus 로고    scopus 로고
    • Building a scalable bipartite P2P overlay network
    • DOI 10.1109/TPDS.2007.1059
    • 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)
    • (2007) IEEE Transactions on Parallel and Distributed Systems , vol.18 , Issue.9 , pp. 1296-1306
    • Liu, Y.1    Xiao, L.2    Ni, L.M.3
  • 14
    • 43349092363 scopus 로고    scopus 로고
    • CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment
    • DOI 10.1186/1471-2105-9-S2-S10
    • CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment. SA Manavski G Valle, BMC Bioinformatics 2008 9 Suppl 2 10 18387198 10.1186/1471-2105-9-S2-S10 (Pubitemid 351944013)
    • (2008) BMC Bioinformatics , vol.9 , Issue.SUPPL. 2
    • Manavski, S.A.1    Valle, G.2
  • 15
    • 0030935244 scopus 로고    scopus 로고
    • Using video-oriented instructions to speed up sequence comparison
    • 9146961
    • Using video-oriented instructions to speed up sequence comparison. A Wozniak, Comput Appl Biosci 1997 13 2 145 150 9146961
    • (1997) Comput Appl Biosci , vol.13 , Issue.2 , pp. 145-150
    • Wozniak, A.1
  • 16
    • 0033743209 scopus 로고    scopus 로고
    • Six-fold speedup of Smith-Waterman sequence database searches using parallel processing on common microprocessors
    • 11099256. 10.1093/bioinformatics/16.8.699
    • 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 11099256 10.1093/bioinformatics/16.8.699
    • (2000) Bioinformatics , vol.16 , Issue.8 , pp. 699-706
    • Rognes, T.1    Seeberg, E.2
  • 17
    • 78651550268 scopus 로고    scopus 로고
    • Scalable parallel programming with CUDA
    • 10.1145/1365490.1365500
    • Scalable Parallel Programming with CUDA. J Nickolls I Buck M Garland K Skadron, ACM Queue 2008 6 2 40 53 10.1145/1365490.1365500
    • (2008) ACM Queue , vol.6 , Issue.2 , pp. 40-53
    • Nickolls, J.1    Buck, I.2    Garland, M.3    Skadron, K.4
  • 18
    • 44849137198 scopus 로고    scopus 로고
    • NVIDIA Tesla: A unified graphics and computing architecture
    • DOI 10.1109/MM.2008.31
    • 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)
    • (2008) IEEE Micro , vol.28 , Issue.2 , pp. 39-55
    • Lindholm, E.1    Nickolls, J.2    Oberman, S.3    Montrym, J.4
  • 19
    • 77049105079 scopus 로고    scopus 로고
    • P Green, http://www.phrap.org/phredphrap/swat.html
    • P Green, http://www.phrap.org/phredphrap/swat.html
  • 20
    • 77049126343 scopus 로고    scopus 로고
    • NVIDIA CUDA programming guide 2.0. http://developer.download.nvidia.com/ compute/cuda/2-0/docs/NVIDIA-CUDA-Programming-Guide-2.0.pdf
    • NVIDIA CUDA Programming Guide 2.0


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.