Bayesian Models for Multiple Local Sequence Alignment and Gibbs Sampling Strategies

References

• Akaike , H. “Information Theory and the Maximum Likelihood Principle,” . 2nd International Symposium on Information Theory . Edited by: Petrov , B. N. and Csàki , F. Budapest : Akademiai Kiàdo .
   Google Scholar
• Allison , L. , Wallace , C. S. and Yee , C. N. “Minimum Message Length Encoding Evolutionary Trees and Multiple Alignment,” . Proceedings of 25th Hawaii International Conference on System Science . pp. 663 – 674 .
   Google Scholar
• Altschul , S. F. , Gish , W. , Miller , M. , Myers , E. W. and Lipman , D. J. 1990 . “Basic Local Alignment Search Tool,” . Journal of Molecular Biology , 215 : 403 – 410 .
   PubMed Web of Science ®Google Scholar
• Baldi , P. , Chauvin , Y. , McClure , M. and Hunkapiller , T. 1994 . “Hidden Markov Models of Biological Primary Sequence Information,” . Proceedings of the National Academy of Science of USA , 91 : 1059 – 1063 .
   PubMed Web of Science ®Google Scholar
• Berg , O. G. and vonHippie , P. H. 1987 . “Selection of DNA Binding Sites by Regulatory Proteins: Statistical-Mechanical Theory and Application to Operators and Promoters,” . Journal of Molecular Biology , 193 : 153 – 161 .
   Web of Science ®Google Scholar
• Bishop , M. J. and Thompson , E. A. 1986 . “Maximum Likelihood Alignment of DNA Sequences,” . Journal of Molecular Biology , 190 : 159 – 165 .
   PubMed Web of Science ®Google Scholar
• Bryant , S. H. and Lawrence , C. E. 1991 . “The Frequencies of Ion Pair Substructures in Proteins Is Quantitatively Related to Electrostatic Potentials: A Statistical Model for Nonbonded Interactions,” . PROTEINS: Structure, Function, and Genetics , 9 : 108 – 119 .
   PubMed Web of Science ®Google Scholar
• Bryant , S. H. and Lawrence , C. E. 1993 . “An Empirical Energy Function for Threading Protein Sequence Through the Folding Motif,” . PROTEINS: Structure, Function, and Genetics , 16 : 92 – 112 .
   PubMed Web of Science ®Google Scholar
• Cardon , L. R. and Stormo , G. D. 1992 . “An Expectation Maximization Algorithms for Identifying Protein Binding Sites With Variable Gaps From Unaligned DNA Fragments,” . Journal of Molecular Biology , 223 : 159 – 170 .
   PubMed Web of Science ®Google Scholar
• Chen , R. and Liu , J. S. 1996 . “Predictive Updating Methods With Applications to Bayesian Classification,” . Journal of the Royal Statistical Society , Ser. B, to appear
   Google Scholar
• Chen , X. , Dempster , A. P. and Liu , J. S. 1994 . “Weighted Finite Population Sampling to Maximize Entropy,” . Biometrika , : 457 – 469 .
   Web of Science ®Google Scholar
• Cover , T. M. and Thomas , J. A. 1991 . Elements of Information Theory , New York : John Wiley .
   Google Scholar
• Gelfand , A. E. and Smith , A. F. M. 1990 . “Sampling-Based Approaches to Calculating Marginal Densities,” . Journal of the American Statistical Association , 85 : 398 – 409 .
   Web of Science ®Google Scholar
• Gelman , A. and Rubin , D. B. 1992 . “Inference From Iterative Simulation Using Multiple Sequences,” . Statistical Science , 7 : 457 – 472 .
   Google Scholar
• Haussler , D. , Krogh , A. , Mian , S. and Sjolander , K. “Protein Modeling Using Hidden Markov Models: Analysis of Globins,” . Proceedings of the Hawaii International Conference on System Sciences . Los Alamitos , CA : IEEE Computer Society Press .
   Google Scholar
• Hope , A. C. A. 1968 . “A Simplified Monte Carlo Significance Test Procedure,” . Journal of the Royal Statistical Society , 30 : 582 – 598 . Ser. B
   Google Scholar
• Lawrence , C. E. , 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 – 314 .
   PubMed Web of Science ®Google Scholar
• Lawrence , C. E. and Reilly , A. A. 1990 . “An Expectation Maximization Algorithm for the Identification and Characterization of Common Sites in Unaligned Biopolymer Sequences,” . PROTEINS: Structure, Function, and Genetics , 7 : 41 – 51 .
   PubMed Web of Science ®Google Scholar
• Lawrence , C. E. and Reilly , A. A. 1992 . “Likelihood Inferences With Uncertain Indices With Application to Gene Regulation,” , Biometrics Laboratory, Wadsworth Center for Laboratories and Research. New York State Department of Health . Technical Report 121
   Google Scholar
• Li , K.-H. 1988 . “Imputation Using Markov Chains,” . Journal of Statistical Computation and Simulation , 30 : 57 – 79 .
   Google Scholar
• Lipman , D. J. , Wilbur , W. J. , Smith , T. F. and Waterman , M. S. 1984 . “On the Statistical Significance of Nucleic Acid Similarities,” . Nucleic-Acids Research , 12 : 215226
   Web of Science ®Google Scholar
• Liu , J. S. 1994 . “The Collapsed Gibbs Sampler in Bayesian Computations With Applications to a Gene Regulation Problem,” . Journal of the American Statistical Association , 89 : 958 – 966 .
   Web of Science ®Google Scholar
• Liu , J. S. , Wong , W. H. and Kong , A. 1994 . “Covariance Structure of the Gibbs Sampler With Applications to the Comparisons of Estimators and Augmentation Schemes,” . Biometrika , 81 : 27 – 40 .
   Web of Science ®Google Scholar
• Liu , J. S. , Wong , W. H. and Kong , A. 1995 . “Covariance Structure and Convergence Rate of the Gibbs Sampler With Various Scans,” . Journal of the Royal Statistical Society , 56 : 157 – 169 . Ser. B
   Google Scholar
• Neuwald , A. F. and Green , P. 1994 . “Detecting Patterns in Protein Sequences,” . Journal of Molecular Biology , 239 : 698 – 712 .
   PubMed Web of Science ®Google Scholar
• Neuwald , A. F. , Liu , J. S. and Lawrence , C. E. 1995 . “Sequence Analysis Using a Motif Sampling Strategy,” submitted to Protein Science.
   Google Scholar
• Pohl , F. M. 1971 . “Empirical Protein Energy Maps,” . Nature: New Biology , 234 : 277 – 379 .
   PubMedGoogle Scholar
• Schwartz , G. 1978 . “Estimating the Dimension of a Model,” . The Annals of Statistics , 6 : 461 – 464 .
   Web of Science ®Google Scholar
• Tanner , M. A. and Wong , W. H. 1987 . “The Calculation of Posterior Distribution by Data Augmentation,” . Journal of the American Statistical Association , 82 : 528 – 550 . (with discussion)
   Web of Science ®Google Scholar
• Thorne , J. L. , Kishino , H. and Felsenstein , J. 1991 . “An Evolutionary Model for Maximum Likelihood Alignment of DNA Sequences,” . Journal of Molecular Evolution , 33 : 114 – 124 .
   PubMed Web of Science ®Google Scholar
• Thorne , J. L. , Kishino , H. and Felsenstein . 1992 . “Inching Toward Reality: An Improved Likelihood Model of Sequence Evolution,” . Journal of Molecular Evolution , 34 : 3 – 16 .
   PubMed Web of Science ®Google Scholar
• Tierney , L. 1995 . “Markov Chains for Exploring Posterior Distributions (with discussion),” . The Annals of Statistics , 22 : 1701 – 1762 .
   Web of Science ®Google Scholar
• Wierenga , R. K. , DeMaeyer , M. C. H. and Hol , W. G. J. 1985 . “Interaction of Pyrophosphate Moieties With Alpha-Helixes in Dinucleotide Binding Proteins,” . Biochemistry , 24 : 1346 – 1357 .
   Web of Science ®Google Scholar
• Wilcoxon , F. 1945 . “Individual Comparisons by Ranking Methods,” . Biometrics , 1 : 80 – 83 .
   Web of Science ®Google Scholar