Solvable models of neighbor-dependent substitution processes

Mathematical Biosciences

Volumn 211, Issue 1, 2008, Pages 56-88

  Bérard, Jean ^a,b   Gouéré, Jean Baptiste ^c   Piau, Didier ^d  

^a UNIVERSITÉ LYON 1   (France)

^b UNIVERSITÉ DE LYON   (France)

^c UNIVERSITÉ D'ORLÉANS   (France)

^d INSTITUT FOURIER   (France)

Author keywords

CpG deficiency; Exactly solvable models; Stochastic models of nucleotide substitution

Indexed keywords

DNA; MARKOV PROCESSES; MOLECULAR BIOLOGY; NITROGEN COMPOUNDS; NUCLEOTIDES;

NUCLEOTIDIC SUBSTITUTIONS; PURINES; PYRIMIDINES;

SUBSTITUTION REACTIONS;

DNA;

BIOLOGY; DNA; MARKOV CHAIN; MODELING; STOCHASTICITY;

AMINO ACID SUBSTITUTION; ARTICLE; LINEAR SYSTEM; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; NUCLEOTIDE SEQUENCE; POISSON DISTRIBUTION; PROCESS MODEL;

EID: 37349028659     PISSN: 00255564     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mbs.2007.10.001     Document Type: Article

References (12)

1. Cornish-Bowden A. Nomenclature for incompletely specified bases in nucleic acid sequences recommendations, 1984. Nucleic Acids Res. 13 9 (1985) 3021. http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html Available from: http://www.chem.qmul.ac.uk/iubmb/misc/naseq.html. Also published as: Nomenclature Committee of the International Union of Biochemistry, Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences: Recommendations 1984, Proceedings of the National Academy of Sciences of the USA 83 (1) (1986) 4-8. Available from: http://www.pnas.org/cgi/reprint/83/1/4
2. Duret L., and Galtier N. The covariation between TpA deficiency, CpG deficiency, and G+C content of human isochores is due to a mathematical artifact. Mol. Biol. Evol. 17 (2000) 1620. http://mbe.oxfordjournals.org/cgi/content/full/17/11/1620 Available from:
3. Arndt P.F. Identification and measurement of neighbor dependent nucleotide substitution processes. Lect. Notes Inform. P53 (2004) 227. http://www.molgen.mpg.de/%7Earndt/publications Available from:
4. Arndt P.F., Burge C.B., and Hwa T. DNA sequence evolution with neighbor-dependent mutation. J. Comput. Biol. 10 (2003) 313. Available from arXiv: physics/0112029
5. Arndt P.F., and Hwa T. Identification and measurement of neighbor-dependent nucleotide substitution processes. Bioinformatics 21 (2005) 2322. Available from arXiv: q-bio.GN/0501018
6. Rzhetsky A., and Nei M. Tests of applicability of several substitution models for DNA sequence data. Mol. Biol. Evol. 12 (1995) 131. http://mbe.oxfordjournals.org/cgi/content/abstract/12/1/131 Available from:
7. Lake J.A. A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony. Mol. Biol. Evol. 4 (1987) 167. http://mbe.oxfordjournals.org/cgi/content/abstract/4/2/167 Available from:
8. Navidi W.C., and Beckett-Lemus L. The effect of unequal transversion rates on the accuracy of evolutionary parsimony. Mol. Biol. Evol. 9 (1992) 1163. http://mbe.oxfordjournals.org/cgi/content/abstract/9/6/1163 Available from:
9. Liggett T.M. Interacting Particle Systems (2005), Springer, Berlin Reprint of the 1985 original
10. Rotman J.J. An introduction to the theory of groups. Graduate Texts in Mathematics. Fourth ed. vol. 148 (1995), Springer-Verlag, New York
11. Propp J.G., and Wilson D.B. Exact sampling with coupled Markov chains and applications to statistical mechanics. Proceedings of the Seventh International Conference on Random Structures and Algorithms (Atlanta, GA, 1995). Random Structures Algorithms 9 1-2 (1996) 223. http://dbwilson.com/exact Available from:
12. J. Bérard, J.-B. Gouéré, D. Piau, Solvable models of neighbor-dependent substitution processes. ArXiv e-print (2005). Available from arXiv: math.PR/0510034.