Markovian Models for DNA sequences

[1]  T. Kirkwood,et al.  Statistical Analysis of Deoxyribonucleic Acid Sequence Data-a Review , 1989 .

[2]  E. Lander,et al.  Construction of multilocus genetic linkage maps in humans. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Eugene W. Myers,et al.  A whole-genome assembly of Drosophila. , 2000, Science.

[4]  Leonidas J. Guibas,et al.  String Overlaps, Pattern Matching, and Nontransitive Games , 1981, J. Comb. Theory A.

[5]  Pavel A. Pevzner,et al.  Nucleotide Sequences Versus Markov Models , 1992, Comput. Chem..

[6]  Arthur Nádas Good, Jekinek, Mercer, and Robbins on Turing's Estimate of Probabilities , 1991 .

[7]  M. Waterman,et al.  Statistical characterization of nucleic acid sequence functional domains. , 1983, Nucleic acids research.

[8]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[9]  S. Salzberg,et al.  Microbial gene identification using interpolated Markov models. , 1998, Nucleic acids research.

[10]  L. Alphey DNA Sequencing: From Experimental Methods to Bioinformatics , 1997 .

[11]  Torkel Erhardsson,et al.  Compound Poisson Approximation for Markov Chains using Stein’s Method , 1999 .

[12]  Mark Borodovsky,et al.  First and second moment of counts of words in random texts generated by Markov chains , 1992, Comput. Appl. Biosci..

[13]  Wentian Li,et al.  The Study of Correlation Structures of DNA Sequences: A Critical Review , 1997, Comput. Chem..

[14]  Mark Borodovsky,et al.  GENMARK: Parallel Gene Recognition for Both DNA Strands , 1993, Comput. Chem..

[15]  J. Fickett,et al.  Assessment of protein coding measures. , 1992, Nucleic acids research.

[16]  L. Hood,et al.  Large-scale and automated DNA sequence determination. , 1991, Science.

[17]  R. Ivarie,et al.  Mono- through hexanucleotide composition of the Escherichia coli genome: a Markov chain analysis. , 1987, Nucleic acids research.

[18]  S. Tavaré,et al.  Codon preference and primary sequence structure in protein-coding regions. , 1989, Bulletin of mathematical biology.

[19]  P. Bühlmann,et al.  Variable Length Markov Chains: Methodology, Computing, and Software , 2004 .

[20]  A. Raftery,et al.  Estimation and Modelling Repeated Patterns in High Order Markov Chains with the Mixture Transition Distribution Model , 1994 .

[21]  H Almagor,et al.  A Markov analysis of DNA sequences. , 1983, Journal of theoretical biology.

[22]  Timothy B. Stockwell,et al.  The Sequence of the Human Genome , 2001, Science.

[23]  T P Speed,et al.  Atypical regions in large genomic DNA sequences. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Richard Cowan,et al.  Expected frequencies of DNA patterns using whittle's formula , 1991, Journal of Applied Probability.

[25]  G. Blom,et al.  How many random digits are required until given sequences are obtained? , 1982, Journal of Applied Probability.

[26]  P W Garden,et al.  Markov analysis of viral DNA/RNA sequences. , 1980, Journal of theoretical biology.

[27]  B S Weir Statistical analysis of molecular genetic data. , 1985, IMA journal of mathematics applied in medicine and biology.

[28]  Jean-Jacques Daudin,et al.  Exact distribution of word occurrences in a random sequence of letters , 1999, Journal of Applied Probability.

[29]  Gesine Reinert,et al.  Probabilistic and Statistical Properties of Words: An Overview , 2000, J. Comput. Biol..

[30]  Daniel A. Henderson,et al.  Fitting Markov chain models to discrete state series such as DNA sequences , 1999 .

[31]  Gunnar Blom,et al.  Problems and Snapshots from the World of Probability , 1993 .

[32]  U Grob,et al.  Statistical analysis of nucleotide sequences. , 1990, Nucleic acids research.

[33]  R. Mullin,et al.  The distribution of the frequency of occurrence of nucleotide subsequences, based on their overlap capability. , 1989, Biometrics.

[34]  Bernard Prum,et al.  Finding words with unexpected frequencies in deoxyribonucleic acid sequences , 1995 .

[35]  S. Salzberg,et al.  Improved microbial gene identification with GLIMMER. , 1999, Nucleic acids research.