메뉴 건너뛰기




Volumn 15, Issue 3, 1999, Pages 211-218

DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; COMPUTER PROGRAM; CONFERENCE PAPER; GENETIC PROCEDURES; PERFORMANCE; PRIORITY JOURNAL; TIME;

EID: 0032945593     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/15.3.211     Document Type: Conference Paper
Times cited : (582)

References (34)
  • 2
    • 0022897983 scopus 로고
    • A nonlinear measure of subalignment similarity and its significance levels
    • Altschul, S.F. and Erickson, B.W. (1986) A nonlinear measure of subalignment similarity and its significance levels. Bull. Math. Biol., 48, 617-632.
    • (1986) Bull. Math. Biol. , vol.48 , pp. 617-632
    • Altschul, S.F.1    Erickson, B.W.2
  • 4
    • 0022474446 scopus 로고
    • Maximum likelihood alignment of DNA sequences
    • Bishop, M.J. and Thompson, E.A. (1986) Maximum likelihood alignment of DNA sequences. J. Mol. Biol., 190, 159-165.
    • (1986) J. Mol. Biol. , vol.190 , pp. 159-165
    • Bishop, M.J.1    Thompson, E.A.2
  • 5
    • 0031850192 scopus 로고    scopus 로고
    • Comparative analysis of seven multiple protein sequence alignment servers: Clues to enhance reliability of predictions
    • Briffeuil, P., Baudoux, G., Lambert, C., De Bolle, X., Vinals, C., Feytmans, E. and Depiereux, E. (1998) Comparative analysis of seven multiple protein sequence alignment servers: clues to enhance reliability of predictions. Bioinformatics, 14, 357-366.
    • (1998) Bioinformatics , vol.14 , pp. 357-366
    • Briffeuil, P.1    Baudoux, G.2    Lambert, C.3    De Bolle, X.4    Vinals, C.5    Feytmans, E.6    Depiereux, E.7
  • 6
    • 0032512801 scopus 로고    scopus 로고
    • A symmetric-iterated multiple alignment of protein sequences
    • Brocchieri, L. and Karlin, S. (1998) A symmetric-iterated multiple alignment of protein sequences. J. Mol. Biol., 276, 249-264.
    • (1998) J. Mol. Biol. , vol.276 , pp. 249-264
    • Brocchieri, L.1    Karlin, S.2
  • 7
    • 0024297354 scopus 로고
    • Multiple sequence alignment with hierarchical clustering
    • Corpet, F. (1988) Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res., 16, 10881-10890.
    • (1988) Nucleic Acids Res. , vol.16 , pp. 10881-10890
    • Corpet, F.1
  • 8
    • 0026668613 scopus 로고
    • Match-Box: A fundamentally new algorithm for the simultaneous alignment of several protein sequences
    • Depiereux, E. and Feytmans, E. (1992) Match-Box: a fundamentally new algorithm for the simultaneous alignment of several protein sequences. Comput. Applic. Biosci., 8, 501-509.
    • (1992) Comput. Applic. Biosci. , vol.8 , pp. 501-509
    • Depiereux, E.1    Feytmans, E.2
  • 10
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff, S. and Henikoff, J.G. (1992) Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA, 89, 10915-10919.
    • (1992) Proc. Natl Acad. Sci. USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 11
    • 0028304908 scopus 로고
    • On global sequence alignment
    • Huang, X. (1994) On global sequence alignment. Comput. Appl. Biosci. 10, 227-235.
    • (1994) Comput. Appl. Biosci. , vol.10 , pp. 227-235
    • Huang, X.1
  • 12
    • 0029935769 scopus 로고    scopus 로고
    • Evolutionary conservation of RecA genes in relation to protein structure and function
    • Karlin, S. and Brocchieri, L. (1996) Evolutionary conservation of RecA genes in relation to protein structure and function. J. Bacteriol., 178, 1881-1894.
    • (1996) J. Bacteriol. , vol.178 , pp. 1881-1894
    • Karlin, S.1    Brocchieri, L.2
  • 13
    • 0027912333 scopus 로고
    • Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
    • Lawrence, C.E., Altschul, S.F., Boguski, M.S., Lin, J.S., Neuwald, A.F. and Wootton, J.C. (1993) Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment. Science, 262, 208-213.
    • (1993) Science , vol.262 , pp. 208-213
    • Lawrence, C.E.1    Altschul, S.F.2    Boguski, M.S.3    Lin, J.S.4    Neuwald, A.F.5    Wootton, J.C.6
  • 14
    • 0032892093 scopus 로고    scopus 로고
    • Exact solutions for the segment-to-segment multiple alignment problem
    • Lenhof, H.-P., Morgenstern, B. and Reinert, K. (1999) Exact solutions for the segment-to-segment multiple alignment problem. Bioinformatics, 15, 203-210.
    • (1999) Bioinformatics , vol.15 , pp. 203-210
    • Lenhof, H.-P.1    Morgenstern, B.2    Reinert, K.3
  • 15
    • 0028341506 scopus 로고
    • Comparative analysis of multiple protein-sequence alignment methods
    • McClure, M.A., Vasi, T.K. and Fitch, W.M. (1994) Comparative analysis of multiple protein-sequence alignment methods. Mol. Biol. Evol., 11, 571-592.
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 571-592
    • McClure, M.A.1    Vasi, T.K.2    Fitch, W.M.3
  • 16
    • 0029861894 scopus 로고    scopus 로고
    • Multiple DNA and protein sequence alignment based on segment-to-segment comparison
    • Morgenstern, B., Dress, A. and Werner, T. (1996) Multiple DNA and protein sequence alignment based on segment-to-segment comparison. Proc. Natl Acad. Sci. USA, 93, 12098-12103.
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 12098-12103
    • Morgenstern, B.1    Dress, A.2    Werner, T.3
  • 17
    • 0031854952 scopus 로고    scopus 로고
    • DIALIGN: Finding local similarities by multiple sequence alignment
    • Morgenstern, B., Frech, K., Dress, A. and Werner, T. (1998a) DIALIGN: Finding local similarities by multiple sequence alignment. Bioinformatics, 14, 290-294.
    • (1998) Bioinformatics , vol.14 , pp. 290-294
    • Morgenstern, B.1    Frech, K.2    Dress, A.3    Werner, T.4
  • 18
    • 0031604259 scopus 로고    scopus 로고
    • Segment-based scores for pairwise and multiple sequence alignments
    • Glasgow, J., Littlejohn, T., Major, F., Lathrop, R., Sankoff, D. and Sensen, C. (eds). AAAI Press, Menlo Park, CA.
    • Morgenstern, B., Atchley, W.R., Hahn, K. and Dress, A. (1998b) Segment-based scores for pairwise and multiple sequence alignments. In Glasgow, J., Littlejohn, T., Major, F., Lathrop, R., Sankoff, D. and Sensen, C. (eds), Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA. pp. 115-121.
    • (1998) Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology , pp. 115-121
    • Morgenstern, B.1    Atchley, W.R.2    Hahn, K.3    Dress, A.4
  • 19
    • 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. (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
    • (1970) J. Mol. Biol. , vol.48 , pp. 443-453
    • Needleman, S.1    Wunsch, C.2
  • 20
    • 0028270992 scopus 로고
    • Detecting patterns in protein sequences
    • Neuwald, A.F. and Green, P. (1994) Detecting patterns in protein sequences. J. Mol. Biol., 239, 698-712.
    • (1994) J. Mol. Biol. , vol.239 , pp. 698-712
    • Neuwald, A.F.1    Green, P.2
  • 21
    • 0029872694 scopus 로고    scopus 로고
    • SAGA: Sequence alignment by genetic algorithm
    • Notredame, C. and Higgins, D.H. (1996) SAGA: sequence alignment by genetic algorithm. Nucleic Acids Res., 24, 1515-1524.
    • (1996) Nucleic Acids Res. , vol.24 , pp. 1515-1524
    • Notredame, C.1    Higgins, D.H.2
  • 22
    • 0023989064 scopus 로고
    • Improved tools for biological sequence comparison
    • Pearson, W.R. and Lipman, D.J. (1988) Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA, 85, 2444-2448.
    • (1988) Proc. Natl Acad. Sci. USA , vol.85 , pp. 2444-2448
    • Pearson, W.R.1    Lipman, D.J.2
  • 25
    • 40849099796 scopus 로고
    • Comparison of biosequences
    • Smith, T. and Waterman, M. (1981) Comparison of biosequences. Adv. Appl. Math., 2, 482-489.
    • (1981) Adv. Appl. Math. , vol.2 , pp. 482-489
    • Smith, T.1    Waterman, M.2
  • 26
    • 0025141443 scopus 로고
    • Automatic generation of primary sequence patterns from sets of related protein sequences
    • Smith, R.F. and Smith,T.F. (1990) Automatic generation of primary sequence patterns from sets of related protein sequences. Proc. Natl Acad. Sci. USA, 87, 118-122.
    • (1990) Proc. Natl Acad. Sci. USA , vol.87 , pp. 118-122
    • Smith, R.F.1
  • 27
    • 0345676554 scopus 로고    scopus 로고
    • Multiple sequence alignment with the divide-and-conquer method
    • Stoye, J. (1998) Multiple sequence alignment with the divide-and-conquer method. Gene, 211, GC45-GC56.
    • (1998) Gene , vol.211
    • Stoye, J.1
  • 28
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson, J.D., Higgins, D.G. and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 29
    • 0026528734 scopus 로고
    • Inching toward reality: An improved likelihood model of sequence evolution
    • Thorne, J.L., Kishino, H. and Felsenstein, J. (1992) Inching toward reality: an improved likelihood model of sequence evolution. J. Mol. Evol., 34, 3-16.
    • (1992) J. Mol. Evol. , vol.34 , pp. 3-16
    • Thorne, J.L.1    Kishino, H.2    Felsenstein, J.3
  • 30
    • 0029028454 scopus 로고
    • Estimation and reliability of molecular sequence alignments
    • Thorne, J.L. and Churchill, G.A. (1995) Estimation and reliability of molecular sequence alignments. Biometrics, 51, 100-113.
    • (1995) Biometrics , vol.51 , pp. 100-113
    • Thorne, J.L.1    Churchill, G.A.2
  • 31
    • 0029884395 scopus 로고    scopus 로고
    • A general method for fast multiple sequence alignment
    • Tönges, U., Perrey, S.W., Stoye, J. and Dress, A. (1996) A general method for fast multiple sequence alignment. Gene, 172, GC33-GC41.
    • (1996) Gene , vol.172
    • Tönges, U.1    Perrey, S.W.2    Stoye, J.3    Dress, A.4
  • 32
    • 0023057161 scopus 로고
    • Multiple sequence alignment by consensus
    • Waterman, M.S. (1986) Multiple sequence alignment by consensus. Nucleic Acids Res., 14, 9095-9102.
    • (1986) Nucleic Acids Res. , vol.14 , pp. 9095-9102
    • Waterman, M.S.1
  • 34
    • 0031874740 scopus 로고    scopus 로고
    • Bayesian adaptive sequence alignment algorithms
    • Zhu, J., Lin, J.S. and Lawrence, C.E. (1998) Bayesian adaptive sequence alignment algorithms. Bioinformatics, 14, 25-39.
    • (1998) Bioinformatics , vol.14 , pp. 25-39
    • Zhu, J.1    Lin, J.S.2    Lawrence, C.E.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.