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Volumn 24, Issue 8, 1998, Pages 1177-1204

Parallel computing for chromosome reconstruction via ordering of DNA sequences

Author keywords

Chromosome reconstruction; Clone ordering; DNA sequencing; Parallel processing; Simulated annealing

Indexed keywords

CHROMOSOMES; CONVERGENCE OF NUMERICAL METHODS; DNA SEQUENCES; HEURISTIC METHODS; MARKOV PROCESSES; PARALLEL ALGORITHMS; PERTURBATION TECHNIQUES; SIMULATED ANNEALING;

EID: 0032136075     PISSN: 01678191     EISSN: None     Source Type: Journal    
DOI: 10.1016/s0167-8191(98)00053-2     Document Type: Article
Times cited : (7)

References (55)
  • 3
    • 0025206726 scopus 로고
    • Parallel simulated annealing algorithms for cell placement on the hypercube multiprocessor
    • P. Banerjee, M.H. Jones, J.S. Sargent, Parallel simulated annealing algorithms for cell placement on the hypercube multiprocessor, IEEE Trans. Parallel and Distributed Systems 1 (1990) 91-106.
    • (1990) IEEE Trans. Parallel and Distributed Systems , vol.1 , pp. 91-106
    • Banerjee, P.1    Jones, M.H.2    Sargent, J.S.3
  • 7
    • 38249003815 scopus 로고
    • A parallel simulated annealing algorithm
    • N. Boissin, J.L. Lutton, A parallel simulated annealing algorithm, Parallel Computing 19 (1993) 859-872.
    • (1993) Parallel Computing , vol.19 , pp. 859-872
    • Boissin, N.1    Lutton, J.L.2
  • 8
    • 0017216776 scopus 로고
    • Testing for the consecutive one's property, interval graphs and graph planarity using pq-tree algorithms
    • K.S. Booth, G.S. Lueker, Testing for the consecutive one's property, interval graphs and graph planarity using pq-tree algorithms, J. Comput. Systems Sci. 13 (1976) 335-379.
    • (1976) J. Comput. Systems Sci. , vol.13 , pp. 335-379
    • Booth, K.S.1    Lueker, G.S.2
  • 11
    • 0027723477 scopus 로고
    • A first-generation physical map of the human genome
    • D. Cohen, I. Chumakov, J. Weissenbach, A first-generation physical map of the human genome, Nature 366 (1993) 698-701.
    • (1993) Nature , vol.366 , pp. 698-701
    • Cohen, D.1    Chumakov, I.2    Weissenbach, J.3
  • 12
    • 0000365871 scopus 로고
    • Toward a physical map of the genome of the nematode Caenorhabditis Elegans
    • A. Coulson, J. Sulston, S. Brenner, J. Karn, Toward a physical map of the genome of the nematode Caenorhabditis Elegans, Proc. Natl. Acad. Sci. 83 (1986) 7821-7825.
    • (1986) Proc. Natl. Acad. Sci. , vol.83 , pp. 7821-7825
    • Coulson, A.1    Sulston, J.2    Brenner, S.3    Karn, J.4
  • 13
    • 0023157065 scopus 로고
    • Construction of a general human chromosome jumping library with application to cystic fibrosis
    • F.S. Collins, M.L. Drumm, J.L. Cole, W.K. Lockwood, G.F. Vande Woude, M.C. lanuzzi, Construction of a general human chromosome jumping library with application to cystic fibrosis, Science 235 (1987) 1046-1049.
    • (1987) Science , vol.235 , pp. 1046-1049
    • Collins, F.S.1    Drumm, M.L.2    Cole, J.L.3    Lockwood, W.K.4    Vande Woude, G.F.5    Lanuzzi, M.C.6
  • 14
    • 0027433148 scopus 로고
    • A new five-year plan for the US human genome project
    • F. Collins, D. Galas, A new five-year plan for the US human genome project, Science 262 (1993) 53-56.
    • (1993) Science , vol.262 , pp. 53-56
    • Collins, F.1    Galas, D.2
  • 15
    • 0026782541 scopus 로고
    • The use of simulated annealing in chromosome reconstruction experiments based on binary scoring
    • A.J. Cuticchia, J. Arnold, W.E. Timberlake, The use of simulated annealing in chromosome reconstruction experiments based on binary scoring, Genetics 132 (1992) 591-601.
    • (1992) Genetics , vol.132 , pp. 591-601
    • Cuticchia, A.J.1    Arnold, J.2    Timberlake, W.E.3
  • 16
    • 0027278817 scopus 로고
    • ODS: Ordering DNA sequences - A physical mapping algorithm based on simulated annealing
    • A.J. Cuticchia, J. Arnold, W.E. Timberlake, ODS: Ordering DNA sequences - A physical mapping algorithm based on simulated annealing, CABIOS 9 (1993) 215-219.
    • (1993) CABIOS , vol.9 , pp. 215-219
    • Cuticchia, A.J.1    Arnold, J.2    Timberlake, W.E.3
  • 18
    • 0026726412 scopus 로고
    • The human Y chromosome: Overlapping DNA clones spanning the euchromatic region
    • S. Foote, D. Vollrath, A. Hilton, D.C. Page, The human Y chromosome: Overlapping DNA clones spanning the euchromatic region, Science 258 (1992) 60-66.
    • (1992) Science , vol.258 , pp. 60-66
    • Foote, S.1    Vollrath, D.2    Hilton, A.3    Page, D.C.4
  • 20
    • 0021518209 scopus 로고
    • Stochastic relaxation, Gibbs distribution and the Bayesian restoration of images
    • S. Geman, D. Geman, Stochastic relaxation, Gibbs distribution and the Bayesian restoration of images, IEEE Trans. Pattern Analysis and Machine Intelligence 6 (1984) 721-741.
    • (1984) IEEE Trans. Pattern Analysis and Machine Intelligence , vol.6 , pp. 721-741
    • Geman, S.1    Geman, D.2
  • 21
    • 0024997934 scopus 로고
    • Chromosomal region of the cystic fibrosis gene in yeast artificial chromosomes: A model for human genome mapping
    • F.D. Green, M.V. Olson, Chromosomal region of the cystic fibrosis gene in yeast artificial chromosomes: A model for human genome mapping, Science 250 (1990) 94-98.
    • (1990) Science , vol.250 , pp. 94-98
    • Green, F.D.1    Olson, M.V.2
  • 22
    • 0000759757 scopus 로고
    • Parallel simulated annealing techniques
    • D.R. Greening, Parallel simulated annealing techniques, Physica D 42 (1990) 293-306.
    • (1990) Physica D , vol.42 , pp. 293-306
    • Greening, D.R.1
  • 24
    • 0026519753 scopus 로고
    • Parallelization of a local similarity search algorithm
    • X. Huang, W. Miller, S. Schwartz, R.C. Hardison, Parallelization of a local similarity search algorithm, CABIOS 8 (1992) 155-166.
    • (1992) CABIOS , vol.8 , pp. 155-166
    • Huang, X.1    Miller, W.2    Schwartz, S.3    Hardison, R.C.4
  • 28
    • 0026694927 scopus 로고
    • Sequence pattern matching on a massively parallel computer
    • R. Jones, Sequence pattern matching on a massively parallel computer, CABIOS 8 (1992) 377-384.
    • (1992) CABIOS , vol.8 , pp. 377-384
    • Jones, R.1
  • 29
    • 26444479778 scopus 로고
    • Optimization by simulated annealing
    • S. Kirkpatrick, C. Gelatt Jr., M. Vecchi, Optimization by simulated annealing, Science 220 (4598) (1983) 498-516.
    • (1983) Science , vol.220 , Issue.4598 , pp. 498-516
    • Kirkpatrick, S.1    Gelatt C., Jr.2    Vecchi, M.3
  • 30
    • 0000803318 scopus 로고
    • Construction of multi-locus genetic linkage maps in humans
    • E.S. Lander, P. Green, Construction of multi-locus genetic linkage maps in humans, Proc. Natl. Acad. Sci. 84 (1987) 2363-2367.
    • (1987) Proc. Natl. Acad. Sci. , vol.84 , pp. 2363-2367
    • Lander, E.S.1    Green, P.2
  • 32
    • 0015604699 scopus 로고
    • An effective heuristic for the traveling salesman problem
    • S. Lin, B. Kernighan, An effective heuristic for the traveling salesman problem, Operations Research 21 (1973) 498-516.
    • (1973) Operations Research , vol.21 , pp. 498-516
    • Lin, S.1    Kernighan, B.2
  • 33
    • 0027717575 scopus 로고
    • SIMD parallelization of the WORDUP algorithm for detecting statistically significant patterns in DNA sequences
    • S. Liuni, N. Prunella, G. Pesole, T. D'Orazio, E. Stella, A. Distante, SIMD parallelization of the WORDUP algorithm for detecting statistically significant patterns in DNA sequences, CABIOS 9 (1993) 701-708.
    • (1993) CABIOS , vol.9 , pp. 701-708
    • Liuni, S.1    Prunella, N.2    Pesole, G.3    D'Orazio, T.4    Stella, E.5    Distante, A.6
  • 34
    • 0348019379 scopus 로고
    • MasPar Parallel Applications Language (MPL)
    • MasPar Computer Corp., Sunnyvale, CA
    • MasPar Parallel Applications Language (MPL), Reference Guide, MasPar Computer Corp., Sunnyvale, CA, 1993.
    • (1993) Reference Guide
  • 37
    • 0026538781 scopus 로고
    • Comparing machine-independent versus machine-specific parallelization of a software platform for biological sequence comparison
    • P.L. Miller, P.M. Nadkarni, W.R. Pearson, Comparing machine-independent versus machine-specific parallelization of a software platform for biological sequence comparison, CABIOS 8 (2) (1992) 167-175.
    • (1992) CABIOS , vol.8 , Issue.2 , pp. 167-175
    • Miller, P.L.1    Nadkarni, P.M.2    Pearson, W.R.3
  • 38
    • 0026605535 scopus 로고
    • Harnessing networked workstations as a powerful parallel computer: A general paradigm illustrated using three programs for genetic linkage analysis
    • P.L. Miller, P.M. Nadkarni, P.A. Bercovitz, Harnessing networked workstations as a powerful parallel computer: A general paradigm illustrated using three programs for genetic linkage analysis, CABIOS 8 (2) (1992) 141-147.
    • (1992) CABIOS , vol.8 , Issue.2 , pp. 141-147
    • Miller, P.L.1    Nadkarni, P.M.2    Bercovitz, P.A.3
  • 40
    • 0024980741 scopus 로고
    • A common language for physical mapping of the human genome
    • M.V. Olson, L. Hood, C. Cantor, D. Botstein, A common language for physical mapping of the human genome, Science 245 (1989) 1434-1435.
    • (1989) Science , vol.245 , pp. 1434-1435
    • Olson, M.V.1    Hood, L.2    Cantor, C.3    Botstein, D.4
  • 42
    • 0017495099 scopus 로고
    • The indirect binary N-cube microprocessor array
    • M.C. Pease, The indirect binary N-cube microprocessor array, IEEE Transactions on Computers, C/ 25 (5) (1977) 458-473.
    • (1977) IEEE Transactions on Computers, C , vol.25 , Issue.5 , pp. 458-473
    • Pease, M.C.1
  • 44
    • 0025748279 scopus 로고
    • A theoretical framework for simulated annealing
    • F. Romeo, A. Sangiovanni-Vincentelli, A theoretical framework for simulated annealing, Algorith-mica 6 (1991) 302-345.
    • (1991) Algorith-mica , vol.6 , pp. 302-345
    • Romeo, F.1    Sangiovanni-Vincentelli, A.2
  • 45
    • 0024027033 scopus 로고
    • Mapping of Escherichia coli chromosomal Tn5 and F insertions by pulsed field gel electrophoresis
    • C.L. Smith, R.D. Kolodner, Mapping of Escherichia coli chromosomal Tn5 and F insertions by pulsed field gel electrophoresis, Genetics 119 (1988) 227-236.
    • (1988) Genetics , vol.119 , pp. 227-236
    • Smith, C.L.1    Kolodner, R.D.2
  • 46
    • 0028362302 scopus 로고
    • GRAM and GenfragII: Solving and testing the single-digest, partially ordered restriction map problem
    • C. Soderlund, C. Burks, GRAM and GenfragII: Solving and testing the single-digest, partially ordered restriction map problem, CABIOS 10 (1994) 349-358.
    • (1994) CABIOS , vol.10 , pp. 349-358
    • Soderlund, C.1    Burks, C.2
  • 47
    • 84956762643 scopus 로고
    • The linear arrangement of six sex-linked factors in Drosophila as shown by their mode of association
    • A.H. Sturtevant, The linear arrangement of six sex-linked factors in Drosophila as shown by their mode of association, J. Exp. Zool. 14 (1913) 43-49.
    • (1913) J. Exp. Zool. , vol.14 , pp. 43-49
    • Sturtevant, A.H.1
  • 48
    • 84990637885 scopus 로고
    • PVM: A framework for parallel distributed computing
    • V. Sunderam, PVM: A framework for parallel distributed computing, Concurrency: Practice and Experience 2 (2) (1992) 315-339.
    • (1992) Concurrency: Practice and Experience , vol.2 , Issue.2 , pp. 315-339
    • Sunderam, V.1
  • 49
    • 45949121309 scopus 로고
    • Fast simulated annealing
    • H. Szu, R. Hartley, Fast simulated annealing, Physics Letters A 122 (3/4) (1987) 157-162.
    • (1987) Physics Letters A , vol.122 , Issue.3-4 , pp. 157-162
    • Szu, H.1    Hartley, R.2
  • 50
    • 0023669879 scopus 로고
    • Nonconvex optimization by fast simulated annealing
    • H. Szu, R. Hartley, Nonconvex optimization by fast simulated annealing, Proc. IEEE 75 (11) (1987) 1538-1540.
    • (1987) Proc. IEEE , vol.75 , Issue.11 , pp. 1538-1540
    • Szu, H.1    Hartley, R.2
  • 54
    • 0030061644 scopus 로고    scopus 로고
    • On the consistency of a physical mapping method to reconstruct a chromosome in vitro
    • M. Xiong, H.J. Chen, R.A. Prade, Y. Wang, J. Griffith, W.E. Timberlake, J. Arnold, On the consistency of a physical mapping method to reconstruct a chromosome in vitro, Genetics 142 (1) (1996) 267-284.
    • (1996) Genetics , vol.142 , Issue.1 , pp. 267-284
    • Xiong, M.1    Chen, H.J.2    Prade, R.A.3    Wang, Y.4    Griffith, J.5    Timberlake, W.E.6    Arnold, J.7
  • 55
    • 0028321815 scopus 로고
    • An algorithm based on graph theory for the assembly of contigs in physical mapping of DNA
    • P. Zhang, E.A. Schon, S.G. Fischer, E. Cayanis, J. Weiss, S. Kistler, P.E. Bourne, An algorithm based on graph theory for the assembly of contigs in physical mapping of DNA, CABIOS 10 (1994) 309-317.
    • (1994) CABIOS , vol.10 , pp. 309-317
    • Zhang, P.1    Schon, E.A.2    Fischer, S.G.3    Cayanis, E.4    Weiss, J.5    Kistler, S.6    Bourne, P.E.7


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.