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Volumn , Issue , 2004, Pages 703-708

PROBCONS: Probabilistic consistency-based multiple alignment of amino acid sequences

Author keywords

[No Author keywords available]

Indexed keywords

ALIGNMENT TECHNIQUES; EXPECTATION-MAXIMIZATION (EM); MULTIPLE ALIGNMENT; PROBABILISTIC CONSISTENCY;

EID: 9444254043     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper
Times cited : (23)

References (35)
  • 1
    • 0026786131 scopus 로고
    • Finite-state models in the alignment of macromolecules
    • Allison, L., Wallace, C.S., Yee, C.N. 1992. Finite-state models in the alignment of macromolecules. J Mol Evol 35(1):77-89.
    • (1992) J Mol Evol , vol.35 , Issue.1 , pp. 77-89
    • Allison, L.1    Wallace, C.S.2    Yee, C.N.3
  • 3
    • 0037787816 scopus 로고    scopus 로고
    • The PRINTS database: A resource for identification of protein families
    • Attwood, T.K. 2002. The PRINTS database: a resource for identification of protein families. Brief Bioinform 3(3):252-263.
    • (2002) Brief Bioinform , vol.3 , Issue.3 , pp. 252-263
    • Attwood, T.K.1
  • 4
    • 0000303438 scopus 로고
    • The multiple sequence alignment problem in biology
    • Carrillo, H. and Lipman, D. 1988. The multiple sequence alignment problem in biology. SIAM J Appl Math 48:1073-1082.
    • (1988) SIAM J Appl Math , vol.48 , pp. 1073-1082
    • Carrillo, H.1    Lipman, D.2
  • 7
    • 0023084055 scopus 로고
    • Progressive sequence alignment as a prerequisite to correct phylogenetic trees
    • Feng, D.F., and Doolittle, R.F. 1987. Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J Mol Evol 25:351-360.
    • (1987) J Mol Evol , vol.25 , pp. 351-360
    • Feng, D.F.1    Doolittle, R.F.2
  • 8
    • 0020484488 scopus 로고
    • An improved algorithm for matching biological sequences
    • Gotoh, O. 1982. An improved algorithm for matching biological sequences. J Mol Biol 162:705-708.
    • (1982) J Mol Biol , vol.162 , pp. 705-708
    • Gotoh, O.1
  • 9
    • 0025138774 scopus 로고
    • Consistency of optimal sequence alignments
    • Gotoh, O. 1990. Consistency of optimal sequence alignments. Bull Math Biol 52:509-525.
    • (1990) Bull Math Biol , vol.52 , pp. 509-525
    • Gotoh, O.1
  • 10
    • 0030582739 scopus 로고    scopus 로고
    • Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments
    • Gotoh, O. 1996, Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structural alignments. J Mol Biol 264:823-838.
    • (1996) J Mol Biol , vol.264 , pp. 823-838
    • Gotoh, O.1
  • 11
    • 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 Nat Acad Sci USA 89:10915-10919.
    • (1992) Proc Nat Acad Sci USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 12
    • 0029785147 scopus 로고    scopus 로고
    • Mapping the protein universe
    • Holm, L., and Sander, C. 1996. Mapping the protein universe. Science 273:595-602.
    • (1996) Science , vol.273 , pp. 595-602
    • Holm, L.1    Sander, C.2
  • 13
    • 44949272730 scopus 로고
    • A time-efficient, linear space local similarity algorithm
    • Huang, X., and Miller, W. 1991. A time-efficient, linear space local similarity algorithm. Adv Appl Math 12:337-357.
    • (1991) Adv Appl Math , vol.12 , pp. 337-357
    • Huang, X.1    Miller, W.2
  • 14
    • 0036081436 scopus 로고    scopus 로고
    • In search for more accurate alignments in the twilight zone
    • Jaroszewski, L., Li, W., Godzik, A. 2002. In search for more accurate alignments in the twilight zone. Prot Sci 11(7):1702-1713.
    • (2002) Prot Sci , vol.11 , Issue.7 , pp. 1702-1713
    • Jaroszewski, L.1    Li, W.2    Godzik, A.3
  • 15
    • 0033578684 scopus 로고    scopus 로고
    • Protein secondary structure prediction based on position-specific scoring matrices
    • Jones, D.T. 1999. Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292(2):195-202.
    • (1999) J Mol Biol , vol.292 , Issue.2 , pp. 195-202
    • Jones, D.T.1
  • 16
    • 85010105210 scopus 로고
    • The maximum weight trace problem in multiple sequence alignment
    • Springer-Verlag Lecture Notes in Computer Science
    • Kececioglu, J. 1993. The maximum weight trace problem in multiple sequence alignment. In Proc 4 Symposium on Combinatorial Pattern Matching, Springer-Verlag Lecture Notes in Computer Science 684:106-119.
    • (1993) Proc 4 Symposium on Combinatorial Pattern Matching , vol.684 , pp. 106-119
    • Kececioglu, J.1
  • 17
    • 0027935740 scopus 로고
    • Multiple sequence alignment using simulated annealing
    • Kim, J., Pramanik, S., and Chung, M.J. 1994. Multiple sequence alignment using simulated annealing. Comput Appl Biosci 10(4):419-426.
    • (1994) Comput Appl Biosci , vol.10 , Issue.4 , pp. 419-426
    • Kim, J.1    Pramanik, S.2    Chung, M.J.3
  • 18
    • 0031766401 scopus 로고    scopus 로고
    • HOMSTRAD: A database of protein structure alignments for homologous families
    • Mizuguchi, K., Deane, C.M., Blundell, T.L., and Overington, J.P. 1998. HOMSTRAD: a database of protein structure alignments for homologous families. Prot Sci 7:2469-2471.
    • (1998) Prot Sci , vol.7 , pp. 2469-2471
    • Mizuguchi, K.1    Deane, C.M.2    Blundell, T.L.3    Overington, J.P.4
  • 19
    • 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 Nat Acad Sci USA 93:12098-12103.
    • (1996) Proc Nat Acad Sci USA , vol.93 , pp. 12098-12103
    • Morgenstern, B.1    Dress, A.2    Werner, T.3
  • 20
    • 0031854952 scopus 로고    scopus 로고
    • DIALIGN: Finding local similarities by multiple sequence alignment
    • Morgenstern, B., Frech, K., Dress, A., and Werner, T. 1998. 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
  • 21
    • 0023984847 scopus 로고
    • Optimal alignments in linear space
    • Myers, E.W. and Miller, W. 1988. Optimal alignments in linear space. Comput Appl Biosci 4:11-17.
    • (1988) Comput Appl Biosci , vol.4 , pp. 11-17
    • Myers, E.W.1    Miller, W.2
  • 22
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in amino acid sequence of two proteins
    • Needleman, S.B., and Wunsch, CD. 1970. A general method applicable to the search for similarities in amino acid sequence of two proteins. J Mol Biol 48:443-453.
    • (1970) J Mol Biol , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 23
    • 0029872694 scopus 로고    scopus 로고
    • SAGA: Sequence alignment by genetic algorithm
    • Notredame, C., and Higgins, D.G. 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.G.2
  • 24
    • 0034623005 scopus 로고    scopus 로고
    • T-Coffee: A novel method for multiple sequence alignments
    • Notredame, C., Higgins, D.G., and Heringa, J. 2000. T-Coffee: a novel method for multiple sequence alignments. J Mol Biol 302:205-217.
    • (2000) J Mol Biol , vol.302 , pp. 205-217
    • Notredame, C.1    Higgins, D.G.2    Heringa, J.3
  • 25
    • 0031829993 scopus 로고    scopus 로고
    • COFFEE: An objective function for multiple sequence alignments
    • Notredame, C., Holm, L., and Higgins, D.G. 1998. COFFEE: An objective function for multiple sequence alignments. Bioinformatics 14(5):407-422.
    • (1998) Bioinformatics , vol.14 , Issue.5 , pp. 407-422
    • Notredame, C.1    Holm, L.2    Higgins, D.G.3
  • 26
    • 0033775967 scopus 로고    scopus 로고
    • Multiple sequence alignment in phylogenetic analysis
    • Phillips, A., Janies, D., and Wheeler, W. 2000. Multiple sequence alignment in phylogenetic analysis. Mol Phylogenet Evol 16(3):317-330.
    • (2000) Mol Phylogenet Evol , vol.16 , Issue.3 , pp. 317-330
    • Phillips, A.1    Janies, D.2    Wheeler, W.3
  • 27
    • 0032962457 scopus 로고    scopus 로고
    • Twilight zone of protein sequence alignments
    • Rost, B. 1999. Twilight zone of protein sequence alignments. Protein Eng 12(2):85-94.
    • (1999) Protein Eng , vol.12 , Issue.2 , pp. 85-94
    • Rost, B.1
  • 28
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith, T.F., and Waterman, M.S. 1981. Identification of common molecular subsequences. J Mol Biol 147:195-197.
    • (1981) J Mol Biol , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 29
    • 0031813130 scopus 로고    scopus 로고
    • Pf am: Multiple sequence alignments and HMM-profiles of protein domains
    • Sonnhammer, E.L.L., Eddy, S.R., Birney, E., Bateman, A., and Durbin, R. 1998. Pf am: multiple sequence alignments and HMM-profiles of protein domains. Nucleic Acids Res 26(1):320-322.
    • (1998) Nucleic Acids Res , vol.26 , Issue.1 , pp. 320-322
    • Sonnhammer, E.L.L.1    Eddy, S.R.2    Birney, E.3    Bateman, A.4    Durbin, R.5
  • 30
    • 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
  • 31
    • 0032988850 scopus 로고    scopus 로고
    • BAliBASE: A benchmark alignment database for the evaluation of multiple alignment programs
    • Thompson, J.D., Plewniak, F., and Poch, O. 1999a. BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs. Bioinformatics 15(1):87-88.
    • (1999) Bioinformatics , vol.15 , Issue.1 , pp. 87-88
    • Thompson, J.D.1    Plewniak, F.2    Poch, O.3
  • 32
    • 0033168097 scopus 로고    scopus 로고
    • A comprehensive comparison of multiple sequence alignment programs
    • Thompson, J.D., Plewniak, F., and Poch, O. 1999b. A comprehensive comparison of multiple sequence alignment programs. Nucleic Acids Res 27(13):2682-2690.
    • (1999) Nucleic Acids Res , vol.27 , Issue.13 , pp. 2682-2690
    • Thompson, J.D.1    Plewniak, F.2    Poch, O.3
  • 33
    • 0026036377 scopus 로고
    • Motif recognition and alignment for many sequences by comparison of dot matrices
    • Vingron, M., and Argos, P. 1991. Motif recognition and alignment for many sequences by comparison of dot matrices. J Math Biol 218:34-43.
    • (1991) J Math Biol , vol.218 , pp. 34-43
    • Vingron, M.1    Argos, P.2
  • 34
    • 0024544755 scopus 로고
    • A fast and sensitive multiple sequence alignment algorithm
    • Vingron, M., and Argos, P. 1989. A fast and sensitive multiple sequence alignment algorithm. Comput Appl Biosci 5(2):115-121.
    • (1989) Comput Appl Biosci , vol.5 , Issue.2 , pp. 115-121
    • Vingron, M.1    Argos, P.2
  • 35
    • 0028047892 scopus 로고
    • Sequence alignment and penalty choice: Review of concepts, case studies and implications
    • Vingron, M, and Waterman, M.S. 1994. Sequence alignment and penalty choice: review of concepts, case studies and implications. J Mol Biol 235:1-12.
    • (1994) J Mol Biol , vol.235 , pp. 1-12
    • Vingron, M.1    Waterman, M.S.2


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