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Volumn 2, Issue , 2006, Pages 618-622

Partitioned optimization algorithms for multiple sequence alignment

Author keywords

[No Author keywords available]

Indexed keywords

BENCHMARKING; MOLECULAR BIOLOGY; OPTIMIZATION; PROBLEM SOLVING;

EID: 33751082127     PISSN: 1550445X     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/AINA.2006.260     Document Type: Conference Paper
Times cited : (19)

References (26)
  • 1
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman, S. and Wunsch, C. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48:443-453, 1970.
    • (1970) J. Mol. Biol. , vol.48 , pp. 443-453
    • Needleman, S.1    Wunsch, C.2
  • 3
    • 0031458591 scopus 로고    scopus 로고
    • DCA: An efficient implementation of the divide-andconquer approach to simultaneous multiple sequence alignment
    • Stoye J, Moulton V, Dress AW: DCA: an efficient implementation of the divide-andconquer approach to simultaneous multiple sequence alignment. Comput. Appl. Biosci.13(6), 625-6(1997).
    • (1997) Comput. Appl. Biosci. , vol.13 , Issue.6 , pp. 625-626
    • Stoye, J.1    Moulton, V.2    Dress, A.W.3
  • 4
    • 0033665509 scopus 로고    scopus 로고
    • An iterative method for faster sum-of-pair multiple sequence alignment
    • Reinert K, Stoye J, Will T: An iterative method for faster sum-of-pair multiple sequence alignment. Bioinformatics 16(9),808-814 (2000).
    • (2000) Bioinformatics , vol.16 , Issue.9 , pp. 808-814
    • Reinert, K.1    Stoye, J.2    Will, T.3
  • 5
    • 0000303438 scopus 로고
    • The multiple sequence alignment problem in biology
    • Carrillo H, Lipman DJ: The multiple sequence alignment problem in biology.SIAM J. Appl. Math. 48, 1073-1082 (1988).
    • (1988) SIAM J. Appl. Math. , vol.48 , pp. 1073-1082
    • Carrillo, H.1    Lipman, D.J.2
  • 6
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice
    • 1994
    • Thompson, JD, Higgins, DG and Gibson, TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Research, 1994, vol.22,No.22.4673-4680.
    • (1994) Nucleic Acids Research , vol.22 , Issue.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 7
    • 0023084055 scopus 로고
    • Progressive sequence alignment as a prerequisite to correct phylogenetic trees
    • Feng D-F, Doolittle RF: Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol. 25,351-360(1987)
    • (1987) J. Mol. Evol. , vol.25 , pp. 351-360
    • Feng, D.-F.1    Doolittle, R.F.2
  • 8
    • 0030582739 scopus 로고    scopus 로고
    • Significant improvement in accuracy of multiple protein sequence alignments by iterative refinements as assessed by reference to structural alignments
    • Gotoh O: Significant Improvement in Accuracy of Multiple Protein Sequence Alignments by Iterative Refinements as Assessed by Reference to Structural Alignments. J. Mol. Biol. 264(4), 823-838 (1996).
    • (1996) J. Mol. Biol. , vol.264 , Issue.4 , pp. 823-838
    • Gotoh, O.1
  • 9
    • 0029872694 scopus 로고    scopus 로고
    • SAGA:sequence alignment by genetic algorithm
    • Notredame C, Higgins DG: SAGA:sequence alignment by genetic algorithm. Nucleic Acids Res. 24, 1515-1524 (1996).
    • (1996) Nucleic Acids Res. , vol.24 , pp. 1515-1524
    • Notredame, C.1    Higgins, D.G.2
  • 10
    • 0031854952 scopus 로고    scopus 로고
    • DIALIGN: Finding local similarities by multiple sequence alignment
    • B. Morgenstern and T. Werner (1997) DIALIGN: Finding local similarities by multiple sequence alignment. Bioinformatics 14, 290-294.
    • (1997) Bioinformatics , vol.14 , pp. 290-294
    • Morgenstern, B.1    Werner, T.2
  • 11
    • 0032945593 scopus 로고    scopus 로고
    • DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment
    • 1 March 8
    • Morgenstern B DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics, 1 March 1999, vol.15, no. 3, pp. 211-218(8).
    • (1999) Bioinformatics , vol.15 , Issue.3 , pp. 211-218
    • Morgenstern, B.1
  • 12
    • 77956964275 scopus 로고    scopus 로고
    • An introduction to hidden markov models for biological sequences
    • S. L. Salzberg, D. B. Searls and S. Kasif. Elsevier
    • A.Krogh. An introduction to hidden markov models for biological sequences. In: S. L. Salzberg, D. B. Searls and S. Kasif. Computational Methods in Molecular Biology. Elsevier, 1998:45-63
    • (1998) Computational Methods in Molecular Biology , pp. 45-63
    • Krogh, A.1
  • 13
    • 0036203448 scopus 로고    scopus 로고
    • Multiple sequence alignment using partial order graphs
    • Christopher Lee, Catherine Grasso and Mark F. Sharlow. Multiple sequence alignment using partial order graphs. Bioinformatics, Vol 18 no. 3 2002, pp452-464
    • (2002) Bioinformatics , vol.18 , Issue.3 , pp. 452-464
    • Lee, C.1    Grasso, C.2    Sharlow, M.F.3
  • 14
    • 0037100671 scopus 로고    scopus 로고
    • MAFFT: A novel method for rapid multiple sequence alignment based on fast Fourier transform
    • Jul 15
    • Kazutaka Katoh, Kazuharu Misawal, Kei-ichi Kuma and Takashi Miyata MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 2002 Jul 15;30(14):3059-66
    • (2002) Nucleic Acids Res. , vol.30 , Issue.14 , pp. 3059-3066
    • Katoh, K.1    Misawal, K.2    Kuma, K.-I.3    Miyata, T.4
  • 15
    • 0043285300 scopus 로고    scopus 로고
    • A heuristic algorithm for multiple sequence alignment based on blocks
    • Mar
    • A heuristic algorithm for multiple sequence alignment based on blocks. P.Zhao and Tao Jiang J. Combinatorial Optimization 5(1):95-115, Mar 2001
    • (2001) J. Combinatorial Optimization , vol.5 , Issue.1 , pp. 95-115
    • Zhao, P.1    Jiang, T.2
  • 17
    • 0034623005 scopus 로고    scopus 로고
    • Coffee: A novel method for fast and accurate multiple sequence alignment
    • Sep 8
    • Notredame C, Higgins DG Heringa J T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol. 2000 Sep 8;302(1):205-217
    • (2000) J Mol Biol. , vol.302 , Issue.1 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.T.3
  • 18
    • 13244255415 scopus 로고    scopus 로고
    • MUSCLE: A multiple sequence alignment method with reduced time and space complexity
    • Aug 19
    • Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004 Aug 19;5(1):113.
    • (2004) BMC Bioinformatics , vol.5 , Issue.1 , pp. 113
    • Edgar, R.C.1
  • 19
    • 33751082903 scopus 로고    scopus 로고
    • An adaptive ant colony optimization algorithm and its application to sequence alignment
    • LIANG Dong, HUO Hong-wei. An Adaptive Ant Colony Optimization Algorithm and Its Application to Sequence Alignment. Computer Simulation, 2005, 22(1):100-106.
    • (2005) Computer Simulation , vol.22 , Issue.1 , pp. 100-106
    • Liang, D.1    Huo, H.-W.2
  • 21
    • 0036208872 scopus 로고    scopus 로고
    • Recent progresses in multiple sequence, alignment: A survey
    • C. Notredame, Recent progresses in multiple sequence, alignment: a survey, Pharmacogenomics 3(1) (2002). 131-144
    • (2002) Pharmacogenomics , vol.3 , Issue.1 , pp. 131-144
    • Notredame, C.1
  • 22
    • 0027935740 scopus 로고
    • Multiple sequence alignment using simulated annealing
    • Kim J, Pramanik S, Chung MJ: Multiple Sequence Alignment using Simulated Annealing. Comp. Applic. Biosci. 10(4), 419-426 (1994).
    • (1994) Comp. Applic. Biosci. , vol.10 , Issue.4 , pp. 419-426
    • Kim, J.1    Pramanik, S.2    Chung, M.J.3
  • 23
    • 0033153375 scopus 로고    scopus 로고
    • Allignment of whole genomes
    • Arthur L Delcher, Simon Dasif. Allignment of whole genomes[J]. Nucleic Acids Research, 1999(27):2369-2376
    • (1999) Nucleic Acids Research , Issue.27 , pp. 2369-2376
    • Delcher, A.L.1    Dasif, S.2
  • 25
    • 0023518540 scopus 로고
    • A strategy for the rapid multiple alignment of protein sequences: Confidence levels from tertiary structure comparisons
    • Barton GJ, Sternberg MJE: A strategy for the rapid multiple alignment of protein sequences: confidence levels from tertiary structure comparisons. J. Mol. Biol. 198,327-337 (1987).
    • (1987) J. Mol. Biol. , vol.198 , pp. 327-337
    • Barton, G.J.1    Sternberg, M.J.E.2
  • 26
    • 0026009526 scopus 로고
    • A novel randomized iterative strategy for aligning multiple protein sequences
    • Berger MP, Munson PJ: A novel randomized iterative strategy for aligning multiple protein sequences. Comput. Appl. Biosci. 7,479-484 (1991).
    • (1991) Comput. Appl. Biosci. , vol.7 , pp. 479-484
    • Berger, M.P.1    Munson, P.J.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.