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Volumn 40, Issue 8, 2010, Pages 673-700

Solving longest common subsequence and related problems on graphical processing units

Author keywords

Constrained longest common subsequence; Cuda; General processing using gpu; Graphical processing units; Longest common subsequence; Transposition invariance

Indexed keywords

CONSTRAINED LONGEST COMMON SUBSEQUENCES; CUDA; GENERAL PROCESSING USING GPU; GRAPHICAL PROCESSING UNITS; LONGEST COMMON SUBSEQUENCES; TRANSPOSITION INVARIANCE;

EID: 77956386944     PISSN: 00380644     EISSN: 1097024X     Source Type: Journal    
DOI: 10.1002/spe.976     Document Type: Article
Times cited : (7)

References (52)
  • 1
    • 70349100958 scopus 로고    scopus 로고
    • Khronos OpenCL Working Group, Version 1.0, Document Revision 43, Munshi ed.. Available at:, 16 May
    • Khronos OpenCL Working Group. The OpenCL Specification, Version 1.0, Document Revision 43, Munshi (ed.). Available at: http://www.khronos.org/ registry/cl/specs/opencl-1.0.43pdf [16 May 2009].
    • (2009) The OpenCL Specification
  • 5
    • 62449169653 scopus 로고    scopus 로고
    • Parallel computing with graphics processing units for high-speed Monte Carlo simulation of photon migration
    • Alerstam E, Svensson T, Andersson-Engels S. Parallel computing with graphics processing units for high-speed Monte Carlo simulation of photon migration. Journal of Biomedical Optics 2008;13(6):060504-1-060504-3.
    • (2008) Journal of Biomedical Optics , vol.13 , Issue.6 , pp. 0605041-0605043
    • Alerstam, E.1    Svensson, T.2    Andersson-Engels, S.3
  • 6
    • 60749101535 scopus 로고    scopus 로고
    • A fast hybrid time-synchronous/event approach to parallel discrete event simulation of queuing networks
    • Washington, DC, Mason SJ, Hill RR, Mönch L, Rose O, Jefferson T, Fowler JW eds.
    • Park H, Fishwick PA. A fast hybrid time-synchronous/event approach to parallel discrete event simulation of queuing networks. Proceedings of the 40th Conference on Winter Simulation, Washington, DC, Mason SJ, Hill RR, Mönch L, Rose O, Jefferson T, Fowler JW (eds.), 2008;795-803.
    • (2008) Proceedings of the 40th Conference on Winter Simulation , pp. 795-803
    • Park, H.1    Fishwick, P.A.2
  • 7
    • 77953195609 scopus 로고    scopus 로고
    • NVidia Corporation, Available at:, 18 June
    • NVidia Corporation. CUDA Zone-The Resource for CUDA Developers. Available at: http://www.nvidia.com/object/cuda home.html [18 June 2009].
    • (2009) CUDA Zone-The Resource for CUDA Developers
  • 11
    • 0002650458 scopus 로고    scopus 로고
    • String matching techniques for musical similarity and melodic recognition
    • Crawford T, Iliopoulos C., Raman R. String matching techniques for musical similarity and melodic recognition. Computing in Musicology 1998;11:71-100.
    • (1998) Computing in Musicology , vol.11 , pp. 71-100
    • Crawford, T.1    Iliopoulos, C.2    Raman, R.3
  • 14
    • 33745639010 scopus 로고    scopus 로고
    • Improved time and space complexities for transposition invariant string matching
    • University of Chile, Department of Computer Science, Available at
    • Navarro G, Grabowski Sz, Mäkinen V, Deorowicz S. Improved time and space complexities for transposition invariant string matching. Technical Report TR/DCC-2005-4, University of Chile, Department of Computer Science, 2005;1-11. Available at: ftp://ftp.dcc.uchile.cl/pub/users/gnavarro/mnloglogs.ps.gz.
    • (2005) Technical Report TR/DCC-2005-4 , pp. 1-11
    • Navarro, G.1    Sz, G.2    Mäkinen, V.3    Deorowicz, S.4
  • 15
    • 0142043283 scopus 로고    scopus 로고
    • The constrained common subsequence problem
    • Tsai Y-T. The constrained common subsequence problem. Information Processing Letters 2003;88(4):173-176.
    • (2003) Information Processing Letters , vol.88 , Issue.4 , pp. 173-176
    • Tsai, Y.-T.1
  • 16
    • 77954743402 scopus 로고    scopus 로고
    • Fast algorithm for the constrained longest common subsequence problem
    • Deorowicz S. Fast algorithm for the constrained longest common subsequence problem. Theoretical and Applied Informatics 2007;19(2):91-102.
    • (2007) Theoretical and Applied Informatics , vol.19 , Issue.2 , pp. 91-102
    • Deorowicz, S.1
  • 18
    • 67650552214 scopus 로고    scopus 로고
    • NVidia Corporation, Version 2.2. Available at:, 18 June
    • ™ Programming Guide, Version 2.2. Available at: http://www.nvidia.com/object/cuda get.html [18 June 2009].
    • (2009) ™ Programming Guide
  • 19
    • 77956355697 scopus 로고    scopus 로고
    • CUDA, supercomputing for the masses: Parts 1-15
    • Available at:, 1 March
    • Farber R. CUDA, supercomputing for the masses: Parts 1-15. Doctor Dobb's Journal 2008-2009. Available at: http://www.ddj.com/architect/207200659 [1 March 2010].
    • (2010) Doctor Dobb's Journal 2008-2009
    • Farber, R.1
  • 20
    • 77956376690 scopus 로고    scopus 로고
    • Computing the longest common transposition-invariant subsequence with GPU
    • Cyran KA, Kozielski S, Peters JF, Stanczyk U, Wakulicz-Deja A eds., Springer: Berlin, Heidelberg
    • Deorowicz S. Computing the longest common transposition-invariant subsequence with GPU. Man-Machine Interactions, Series Advances in Intelligent and Soft Computing, Cyran KA, Kozielski S, Peters JF, Stanczyk U, Wakulicz-Deja A (eds.), vol. 59. Springer: Berlin, Heidelberg, 2009;551-559.
    • (2009) Man-Machine Interactions, Series Advances in Intelligent and Soft Computing , vol.59 , pp. 551-559
    • Deorowicz, S.1
  • 22
    • 0016881995 scopus 로고
    • Bounds for the string editing problem
    • Wong CK, Chandra AK. Bounds for the string editing problem. The Journal of the ACM 1976;23(1):13-16.
    • (1976) The Journal of the ACM , vol.23 , Issue.1 , pp. 13-16
    • Wong, C.K.1    Chandra, A.K.2
  • 23
    • 0017492836 scopus 로고
    • A fast algorithm for computing longest common subsequences
    • Hunt JW, Szymanski TG. A fast algorithm for computing longest common subsequences. Communications of the ACM 1977;20(5):350-353.
    • (1977) Communications of the ACM , vol.20 , Issue.5 , pp. 350-353
    • Hunt, J.W.1    Szymanski, T.G.2
  • 24
    • 84976777242 scopus 로고
    • An improved algorithm to find the length of the longest common subsequence of two strings
    • Kuo S, Cross GR. An improved algorithm to find the length of the longest common subsequence of two strings. ACM SIGIR Forum 1989;23%(3-4):89-99.
    • (1989) ACM SIGIR Forum , vol.23 , Issue.3-4 , pp. 89-99
    • Kuo, S.1    Cross, G.R.2
  • 26
    • 0002484064 scopus 로고
    • Preserving order in a forest in less than logarithmic time and linear space
    • van Emde Boas P, Kaas R, Zijlstra E. Preserving order in a forest in less than logarithmic time and linear space. Information Processing Letters 1977;6(3):80-82.
    • (1977) Information Processing Letters , vol.6 , Issue.3 , pp. 80-82
    • Van Emde, B.P.1    Kaas, R.2    Zijlstra, E.3
  • 28
    • 0023041177 scopus 로고
    • A bit-string longest common subsequence algorithm
    • Allison L, Dix TL. A bit-string longest common subsequence algorithm. Information Processing Letters 1986;23(6):305-310.
    • (1986) Information Processing Letters , vol.23 , Issue.6 , pp. 305-310
    • Allison, L.1    Dix, T.L.2
  • 31
    • 33745663723 scopus 로고    scopus 로고
    • Speeding up transposition-invariant string matching
    • Deorowicz S. Speeding up transposition-invariant string matching. Information Processing Letters 2006;100(1):14-20.
    • (2006) Information Processing Letters , vol.100 , Issue.1 , pp. 14-20
    • Deorowicz, S.1
  • 33
    • 0016518550 scopus 로고
    • A linear space algorithm for computing maximal common subsequences
    • Hirschberg DS. A linear space algorithm for computing maximal common subsequences. Communication of the ACM 1975;18(6):341-343.
    • (1975) Communication of the ACM , vol.18 , Issue.6 , pp. 341-343
    • Hirschberg, D.S.1
  • 35
    • 18544379015 scopus 로고    scopus 로고
    • Practical algorithms for transposition-invariant string-matching
    • Lemström K, Navarro G, Pinzon Y. Practical algorithms for transposition-invariant string-matching. Journal of Discrete Algorithms 2005;3%(2-4):267-292.
    • (2005) Journal of Discrete Algorithms , vol.3 , Issue.2-4 , pp. 267-292
    • Lemström, K.1    Navarro, G.2    Pinzon, Y.3
  • 40
    • 77956361181 scopus 로고    scopus 로고
    • An approach for solving the constrained longest common subsequence problem
    • Department of Computer Science and Engineering, National Sun Yat-sen University, Taiwan, Available at:, 1 March
    • Peng Ch-L. An approach for solving the constrained longest common subsequence problem. Master's Thesis, Department of Computer Science and Engineering, National Sun Yat-sen University, Taiwan, 2003;1-29. Available at: http://etd.lib.nsysu.edu.tw/ETD-db/ETD-search/getfile?URN=etd-0828103- 125439&filename=etd-0828103-125439pdf [1 March 2010].
    • (2003) Master's Thesis , pp. 1-29
    • Ch-L, P.1
  • 41
    • 77956387628 scopus 로고    scopus 로고
    • Constrained longest common subsequence computing algorithms in practice
    • Available at:, 1 March, 2010
    • Deorowicz S, Obstój J. Constrained longest common subsequence computing algorithms in practice. Computing and Informatics 2010;29(3). Available at: http://sun. aei.polsl.pl/~sdeor/pub/tr do2009pdf [1 March 2010].
    • (2010) Computing and Informatics , vol.29 , Issue.3
    • Deorowicz, S.1    Obstój, J.2
  • 42
    • 33748534460 scopus 로고    scopus 로고
    • A space-efficient algorithm for the constrained pairwise sequence alignment problem
    • He D, Arslan AN. A space-efficient algorithm for the constrained pairwise sequence alignment problem. Genome Informatics 2005;16(2):237-246.
    • (2005) Genome Informatics , vol.16 , Issue.2 , pp. 237-246
    • He, D.1    Arslan, A.N.2
  • 46
    • 0025467711 scopus 로고
    • A bridging model for parallel computation
    • Valiant LG. A bridging model for parallel computation. Communications of the ACM 1990;33(8):103-111.
    • (1990) Communications of the ACM , vol.33 , Issue.8 , pp. 103-111
    • Valiant, L.G.1
  • 47
    • 33745940915 scopus 로고    scopus 로고
    • Efficient longest common subsequence computation using bulk-synchronous parallelism
    • Krusche P, Tiskin A. Efficient longest common subsequence computation using bulk-synchronous parallelism. Lecture Notes in Computer Science 2006;3984:165-174.
    • (2006) Lecture Notes in Computer Science , vol.3984 , pp. 165-174
    • Krusche, P.1    Tiskin, A.2
  • 49
    • 43349092363 scopus 로고    scopus 로고
    • CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment
    • Available at:, 1 March
    • Manavski SA, Valle G. CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment. BMC Bioinformatics 2008;9(Suppl 2): S10. Available at: http://www.biomedcentral.com/1471-2105/9/S2/ S10 [1 March 2010].
    • (2008) BMC Bioinformatics , vol.9 , Issue.2 SUPPL.
    • Manavski, S.A.1    Valle, G.2
  • 50
    • 70450031959 scopus 로고    scopus 로고
    • An efficient implementation of Smith Waterman algorithm on GPU using CUDA, for massively parallel scanning of sequence databases. ipdps
    • DOI: 10.1109/IPDPS.2009.5160931
    • Ligowski Ł, Rudnicki W. An efficient implementation of Smith Waterman algorithm on GPU using CUDA, for massively parallel scanning of sequence databases. ipdps. IEEE International Symposium on Parallel and Distributed Processing 2009;1-8. DOI: 10.1109/IPDPS.2009.5160931.
    • (2009) IEEE International Symposium on Parallel and Distributed Processing , pp. 1-8
    • Ligowski, Ł.1    Rudnicki, W.2
  • 51
    • 33846697176 scopus 로고    scopus 로고
    • Striped Smith-Waterman speeds database searches six times over other SIMD implementations
    • Farrar M. Striped Smith-Waterman speeds database searches six times over other SIMD implementations. Bioinformatics 2007;23(2):156-161.
    • (2007) Bioinformatics , vol.23 , Issue.2 , pp. 156-161
    • Farrar, M.1
  • 52
    • 77956361381 scopus 로고    scopus 로고
    • Parallel longest common subsequence using graphics hardware
    • Crete, Greece, Favre J, Ma KL, Weiskopf D eds., Available at:, 1 March
    • Kloetzli J, Strege B, Decker J, Olano M. Parallel longest common subsequence using graphics hardware. Proceedings of the Eurographics Symposium on Parallel Graphics and Visualization, Crete, Greece, Favre J, Ma KL, Weiskopf D (eds.), 2008;14-15. Available at: http://www.cs.umbc.edu/~olano/papers/ cudaLCSpdf [1 March 2010].
    • (2008) Proceedings of the Eurographics Symposium on Parallel Graphics and Visualization , pp. 14-15
    • Kloetzli, J.1    Strege, B.2    Decker, J.3    Olano, M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.