Estimating Substitution Matrices

[1]  Durbin,et al.  Biological Sequence Analysis , 1998 .

[2]  M. O. Dayhoff,et al.  Atlas of protein sequence and structure , 1965 .

[3]  John P. Overington,et al.  A structural basis for sequence comparisons. An evaluation of scoring methodologies. , 1993, Journal of molecular biology.

[4]  W J Wilbur,et al.  On the PAM matrix model of protein evolution. , 1985, Molecular biology and evolution.

[5]  Frank Kelly,et al.  Reversibility and Stochastic Networks , 1979 .

[6]  S. Altschul.  Amino acid substitution matrices from an information theoretic perspective , 1991, Journal of Molecular Biology.

[7]  M. Nei,et al.  Statistical properties of the Jukes-Holmquist method of estimating the number of nucleotide substitutions: Reply to Holmquist and Conroy's criticism , 2005, Journal of Molecular Evolution.

[8]  M. Fukushima.  Dirichlet forms and Markov processes , 1980 .

[9]  P. Argos,et al.  An assessment of amino acid exchange matrices in aligning protein sequences: the twilight zone revisited. , 1995, Journal of molecular biology.

[10]  I Holmes,et al.  An expectation maximization algorithm for training hidden substitution models. , 2002, Journal of molecular biology.

[11]  Bruno Torrésani,et al.  Rate Matrices for Analyzing Large Families of Protein Sequences , 2002, J. Comput. Biol..

[12]  H. Ochman,et al.  Strand asymmetries in DNA evolution. , 1997, Trends in genetics : TIG.

[13]  Steven E. Brenner,et al.  Bootstrapping and normalization for enhanced evaluations of pairwise sequence comparison , 2002, Proc. IEEE.

[14]  S. Henikoff,et al.  Amino acid substitution matrices from protein blocks. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[15]  C. Chothia,et al.  Assessing sequence comparison methods with reliable structurally identified distant evolutionary relationships. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[16]  Francesca Chiaromonte,et al.  Scoring Pairwise Genomic Sequence Alignments , 2001, Pacific Symposium on Biocomputing.

[17]  J. Felsenstein.  Cases in which Parsimony or Compatibility Methods will be Positively Misleading , 1978 .

[18]  S A Benner,et al.  Amino acid substitution during functionally constrained divergent evolution of protein sequences. , 1994, Protein engineering.

[19]  Howard Ochman,et al.  Strand Symmetry Around the β-Globin Origin of Replication in Primates , 2000 .

[20]  G. Gonnet,et al.  Exhaustive matching of the entire protein sequence database. , 1992, Science.

[21]  A. Mclachlan.  Tests for comparing related amino-acid sequences. Cytochrome c and cytochrome c 551 . , 1971, Journal of molecular biology.

[22]  R. Gill,et al.  A Survey of Product-Integration with a View Toward Application in Survival Analysis , 1990 .

[23]  P. Lio’,et al.  Models of molecular evolution and phylogeny. , 1998, Genome research.

[24]  Andrew D. Smith,et al.  A Transition Probability Model for Amino Acid Substitutions from Blocks , 2003, J. Comput. Biol..

[25]  Lars Arvestad,et al.  Estimation of Reversible Substitution Matrices from Multiple Pairs of Sequences , 1997, Journal of Molecular Evolution.

[26]  Martin Vingron,et al.  Modeling Amino Acid Replacement , 2000, J. Comput. Biol..

[27]  R. Doolittle,et al.  Aligning amino acid sequences: Comparison of commonly used methods , 1985, Journal of Molecular Evolution.

[28]  D. Rubin,et al.  Maximum likelihood from incomplete data via the EM - algorithm plus discussions on the paper , 1977 .

[29]  Patrick Billingsley,et al.  Statistical inference for Markov processes , 1961 .

[30]  Sven Rahmann,et al.  Non-symmetric score matrices and the detection of homologous transmembrane proteins , 2001, ISMB.

[31]  J. Felsenstein.  Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.

[32]  John B. Fraleigh,et al.  Linear Algebra , 1987 .

[33]  R A Goldstein,et al.  Context-dependent optimal substitution matrices. , 1995, Protein engineering.

[34]  William R. Taylor,et al.  The rapid generation of mutation data matrices from protein sequences , 1992, Comput. Appl. Biosci..

[35]  V. B. Yap,et al.  Modeling DNA Base Substitution in Large Genomic Regions from Two Organisms , 2003, Journal of Molecular Evolution.

[36]  R. Spang,et al.  Estimating amino acid substitution models: a comparison of Dayhoff's estimator, the resolvent approach and a maximum likelihood method. , 2002, Molecular biology and evolution.