메뉴 건너뛰기




Volumn 14, Issue 1, 1998, Pages 25-39

Bayesian adaptive sequence alignment algorithms

Author keywords

[No Author keywords available]

Indexed keywords

GUANOSINE TRIPHOSPHATASE; PHOSPHOTRANSFERASE;

EID: 0031874740     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/14.1.25     Document Type: Article
Times cited : (95)

References (46)
  • 1
    • 0029999739 scopus 로고    scopus 로고
    • A Bayesian evolutionary distance for parameterically aligned sequences
    • Agarwal, P. and States, D.J. (1996) A Bayesian evolutionary distance for parameterically aligned sequences. J. Comput. Biol., 3, 1-17.
    • (1996) J. Comput. Biol. , vol.3 , pp. 1-17
    • Agarwal, P.1    States, D.J.2
  • 2
    • 0026786131 scopus 로고
    • Finite-state models in the alignment of macromolecules
    • Allison, L., Wallace, C.S. and Yee, C.N. (1992) Finite-state models in the alignment of macromolecules. J. Mol. Evol., 35, 77-90.
    • (1992) J. Mol. Evol. , vol.35 , pp. 77-90
    • Allison, L.1    Wallace, C.S.2    Yee, C.N.3
  • 3
    • 0025878149 scopus 로고
    • Amino acid substitution matrices from an information theoretic perspective
    • Altschul, S.F. (1991) Amino acid substitution matrices from an information theoretic perspective. J. Mol. Biol., 219, 555-565.
    • (1991) J. Mol. Biol. , vol.219 , pp. 555-565
    • Altschul, S.F.1
  • 4
    • 0027516090 scopus 로고
    • A protein alignment scoring system sensitive at all evolutionary distances
    • Altschul, S.F. (1993) A protein alignment scoring system sensitive at all evolutionary distances. J. Mol. Evol., 36, 290-300.
    • (1993) J. Mol. Evol. , vol.36 , pp. 290-300
    • Altschul, S.F.1
  • 6
    • 0028685490 scopus 로고
    • Fitting a mixture model by expectation maximization to discover motifs in biopolymers
    • Bailey, T.L. and Elkan, C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. ISMB, 2, 28-36.
    • (1994) ISMB , vol.2 , pp. 28-36
    • Bailey, T.L.1    Elkan, C.2
  • 8
    • 84950900304 scopus 로고
    • Testing a point null hypothesis: The irreconcilability of P values and evidence
    • Berger, J. and Sellke, T. (1987) Testing a point null hypothesis: The irreconcilability of P values and evidence. J. Am Stat. Assoc., 82, 112-122.
    • (1987) J. Am Stat. Assoc. , vol.82 , pp. 112-122
    • Berger, J.1    Sellke, T.2
  • 9
    • 0026026818 scopus 로고
    • The GTPase superfamily: Conserved structure and molecular mechanism
    • Bourne, H.R., Sanders, D.A. and McCormick, F. (1991) The GTPase superfamily: conserved structure and molecular mechanism. Nature, 349, 117-121.
    • (1991) Nature , vol.349 , pp. 117-121
    • Bourne, H.R.1    Sanders, D.A.2    McCormick, F.3
  • 10
    • 0001135785 scopus 로고
    • Sampling and Bayesian inference in scientific modelling and robustness
    • Box, G.E.P. (1980) Sampling and Bayesian inference in scientific modelling and robustness. J. R. Stat. Soc., 143, 383-430.
    • (1980) J. R. Stat. Soc. , vol.143 , pp. 383-430
    • Box, G.E.P.1
  • 13
    • 0028221943 scopus 로고
    • Mutation in the DNA mismatch repair gene homologue hMLH1 is associated with hereditary non-polyposis colon cancer
    • Bronner, C.E. et al. (1994) Mutation in the DNA mismatch repair gene homologue hMLH1 is associated with hereditary non-polyposis colon cancer. Nature, 368, 258-261.
    • (1994) Nature , vol.368 , pp. 258-261
    • Bronner, C.E.1
  • 15
    • 0002929101 scopus 로고
    • A model of evolutionary change in protein
    • Dayhoff, M.E. (ed.), National Biomedical Research Foundation, Washington, DC
    • Dayhoff, M.E., Eck, R.V. and Park, C.M. (1972) A model of evolutionary change in protein. In Dayhoff, M.E. (ed.), Atlas of Protein Sequence and Structure. National Biomedical Research Foundation, Washington, DC, Vol. 5, pp. 89-99.
    • (1972) Atlas of Protein Sequence and Structure , vol.5 , pp. 89-99
    • Dayhoff, M.E.1    Eck, R.V.2    Park, C.M.3
  • 18
    • 0020038367 scopus 로고
    • Pattern recognition in nucleic acid sequences. A general method for finding local homologies and symmetries
    • Goad, W.B. and Kanehisa, M.I. (1982) Pattern recognition in nucleic acid sequences. A general method for finding local homologies and symmetries. Nucleic Acids Res., 10, 247-263.
    • (1982) Nucleic Acids Res. , vol.10 , pp. 247-263
    • Goad, W.B.1    Kanehisa, M.I.2
  • 19
    • 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
  • 20
    • 0027092678 scopus 로고
    • Selection of a representative set of structures from the Brookhaven protein data bank
    • Hobohm, U., Scharf, M., Schneider, R. and Sander, C. (1992) Selection of a representative set of structures from the Brookhaven protein data bank. Protein Sci., 1, 409-417.
    • (1992) Protein Sci. , vol.1 , pp. 409-417
    • Hobohm, U.1    Scharf, M.2    Schneider, R.3    Sander, C.4
  • 21
    • 0028181441 scopus 로고
    • Hidden Markov models in computational biology: Application to protein modelling
    • Krogh, A., Brown, M., Mian, J.S., Sjoelander, K. and Haussler, D. (1994) Hidden Markov models in computational biology: Application to protein modelling. J. Mol. Biol., 235, 1501-1531.
    • (1994) J. Mol. Biol. , vol.235 , pp. 1501-1531
    • Krogh, A.1    Brown, M.2    Mian, J.S.3    Sjoelander, K.4    Haussler, D.5
  • 23
    • 0025320805 scopus 로고
    • An Expectation Maximization (EM) alogrithm for the identification and characterization of common sites in unaligned biopolymer sequences
    • Lawrence, E.C. and Reilly, A.A (1990) An Expectation Maximization (EM) alogrithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins, 7, 41-51.
    • (1990) Proteins , vol.7 , pp. 41-51
    • Lawrence, E.C.1    Reilly, A.A.2
  • 24
    • 0027912333 scopus 로고
    • Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
    • Lawrence, E.C., Altschul, S.F., Boguski, M.S., Liu, J.S., Neuwald, A.F. and Wootton, J.C. (1993) Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment. Science, 262, 208-214.
    • (1993) Science , vol.262 , pp. 208-214
    • Lawrence, E.C.1    Altschul, S.F.2    Boguski, M.S.3    Liu, J.S.4    Neuwald, A.F.5    Wootton, J.C.6
  • 25
    • 0021919480 scopus 로고
    • Rapid and sensitive protein similarity searches
    • Lipman, D.J. and Pearson, W.R. (1985) Rapid and sensitive protein similarity searches. Science, 227, 1435-1441.
    • (1985) Science , vol.227 , pp. 1435-1441
    • Lipman, D.J.1    Pearson, W.R.2
  • 27
    • 0345234230 scopus 로고
    • Statistical models for multiple sequence alignment: Unification and generalization
    • ASA Press, Orlando, FL, Statistical Computation Section 21
    • Liu, J.S. and Lawrence, C.E. (1995) Statistical models for multiple sequence alignment: unification and generalization. In Proceedings of the American Statistical Association. ASA Press, Orlando, FL, Statistical Computation Section 21:1-8.
    • (1995) Proceedings of the American Statistical Association , pp. 1-8
    • Liu, J.S.1    Lawrence, C.E.2
  • 28
    • 0028838717 scopus 로고
    • Threading a database of protein cores
    • Madej, T., Gibrat, J.-F. and Bryant, S.H. (1995) Threading a database of protein cores. Proteins, 23, 356-369.
    • (1995) Proteins , vol.23 , pp. 356-369
    • Madej, T.1    Gibrat, J.-F.2    Bryant, S.H.3
  • 29
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin, A.G., Brenner, S.E.,Hubbard, T. and Chothia, C. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 30
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequences of two proteins
    • Needleman, S.B. and Wunsch, C.D. (1970) A general method applicable to the search for similarities in the amino acid sequences 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
  • 31
    • 0030788541 scopus 로고    scopus 로고
    • Extracting protein alignment models from the sequence database
    • Neuwald, A.F., Liu, J.S., Lipman, D.J. and Lawrence, C.E. (1997) Extracting protein alignment models from the sequence database. Nucleic Acids Res., 25, 1665-1677.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 1665-1677
    • Neuwald, A.F.1    Liu, J.S.2    Lipman, D.J.3    Lawrence, C.E.4
  • 32
    • 0028350601 scopus 로고
    • Mutation of a mutL homolog in hereditary colon cancer
    • Papadopoulos, N. et al. (1994) Mutation of a mutL homolog in hereditary colon cancer. Science, 263, 1625-1629.
    • (1994) Science , vol.263 , pp. 1625-1629
    • Papadopoulos, N.1
  • 33
    • 0025950944 scopus 로고
    • Searching protein sequence libraries: Comparison of the Smith-Waterman and FASTA algorithms
    • Pearson, W.R. (1991) Searching protein sequence libraries: comparison of the Smith-Waterman and FASTA algorithms. Genomics, 11, 635-650.
    • (1991) Genomics , vol.11 , pp. 635-650
    • Pearson, W.R.1
  • 34
    • 0029006770 scopus 로고
    • Comparison of methods for searching protein sequence databases
    • Pearson, W.R. (1995) Comparison of methods for searching protein sequence databases. Protein Sci., 4, 1145-1160.
    • (1995) Protein Sci. , vol.4 , pp. 1145-1160
    • Pearson, W.R.1
  • 35
    • 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
  • 36
    • 0015252494 scopus 로고
    • Matching sequences under deletion/insertion constraints
    • Sankoff, D. (1972) Matching sequences under deletion/insertion constraints. Proc. Natl Acad. Sci. USA, 69, 4-6.
    • (1972) Proc. Natl Acad. Sci. USA , vol.69 , pp. 4-6
    • Sankoff, D.1
  • 37
    • 0000228203 scopus 로고
    • Matrices for detecting distant relationships
    • Dayhoff, M.O. (ed.), National Biomedical Research Foundation, Washington, DC
    • Schwartz, R.M. and Dayhoff, M.O. (1978) Matrices for detecting distant relationships. In Dayhoff, M.O. (ed.), Atlas of Protein Sequence and Structure. National Biomedical Research Foundation, Washington, DC, Vol. 5, Suppl. 3, pp. 353-358.
    • (1978) Atlas of Protein Sequence and Structure , vol.5 , Issue.3 SUPPL. , pp. 353-358
    • Schwartz, R.M.1    Dayhoff, M.O.2
  • 38
    • 0000821965 scopus 로고
    • On the theory and computation of evolutionary distances
    • Sellers, P.H. (1984) On the theory and computation of evolutionary distances. J. Appl. Math., 26, 787-793.
    • (1984) J. Appl. Math. , vol.26 , pp. 787-793
    • Sellers, P.H.1
  • 39
    • 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
  • 40
    • 0027903056 scopus 로고
    • Computationally efficient cluster representation in molecular sequence megaclassification
    • AAAI Press, Bethesda, MD
    • States, D.J., Harris, N.L. and Hunter, L. (1993) Computationally efficient cluster representation in molecular sequence megaclassification. In Proceedings of SMB93. AAAI Press, Bethesda, MD, pp. 387-394.
    • (1993) Proceedings of SMB93 , pp. 387-394
    • States, D.J.1    Harris, N.L.2    Hunter, L.3
  • 41
    • 0026520374 scopus 로고
    • Refined structure of the complex between guanylate kinase and its substrate QMP at 2.0 A resolution
    • Stehle, T. and Schulz, G.E. (1992) Refined structure of the complex between guanylate kinase and its substrate QMP at 2.0 A resolution. J. Mol. Biol., 224, 1127-1141.
    • (1992) J. Mol. Biol. , vol.224 , pp. 1127-1141
    • Stehle, T.1    Schulz, G.E.2
  • 42
    • 0026079507 scopus 로고
    • An evolutionary model for maximum likelihood alignment of DNA sequences
    • Thorne, J., Kishino, H. and Felsenstein, J. (1991) An evolutionary model for maximum likelihood alignment of DNA sequences. J. Mol. Evol., 33, 114-124.
    • (1991) J. Mol. Evol. , vol.33 , pp. 114-124
    • Thorne, J.1    Kishino, H.2    Felsenstein, J.3
  • 43
    • 0026528734 scopus 로고
    • Inching toward reality: An improved likelihood model of sequence evolution
    • Thorne, J., 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.1    Kishino, H.2    Felsenstein, J.3
  • 44
    • 0028464982 scopus 로고
    • Parametric and ensemble sequence alignment algorithms
    • Waterman, M.S. (1994) Parametric and ensemble sequence alignment algorithms. Bull. Math. Biol., 56, 743-767.
    • (1994) Bull. Math. Biol. , vol.56 , pp. 743-767
    • Waterman, M.S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.