Bayesian approach to DNA segmentation into regions with different average nucleotide composition

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 2066, Issue , 2001, Pages 57-73

  Makeev, Vsevolod ^a   Ramensky, Vasily ^a   Gelfand, Mikhail ^b   Roytberg, Mikhail ^c   Tumanyan, Vladimir ^a  

^a ENGELHARDT INSTITUTE OF MOLECULAR BIOLOGY   (Russian Federation)

^b VNIIGENETIKA   (Russian Federation)

^c INSTITUTE OF MATHEMATICAL PROBLEMS OF BIOLOGY   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

BAYESIAN NETWORKS; BIOINFORMATICS; BIOLOGY; INFORMATION SCIENCE;

AVERAGE COMPOSITION; BAYESIAN APPROACHES; CONTEXTUAL EFFECTS; MARGINAL LIKELIHOOD; NUCLEOTIDE COMPOSITION; NUCLEOTIDE SEQUENCES; PARTITION ALGORITHMS; PARTITION FUNCTIONS;

NUCLEOTIDES;

EID: 84959064404     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/3-540-45727-5_6     Document Type: Conference Paper

References (26)

1. Karlin, S., Brendel, V.: Patchiness and correlation in DNA sequences. Science 259 (1993) 677–680.
2. Li, W.: The study of correlation structure of DNA sequences: A critical review. Computer and Chemistry 21(4) (1997) 257–278.
3. Bernardi, G.: The isochore organization of the human genome. Annual Review of Genetics 23 (1989) 637–661.
4. D'Onofrio, G., Mouchiroud, D., Aissani, B., Gautier, C., Bernardi, G.: Correlation between the compositional properties of human genes, codon usage, and amino acid composition of proteins. J. Mol. Evol. 32 (1991) 504–510.
5. Guigo, R. Fickett, J. W.: Distinctive sequence features in protein coding, genic noncoding and intergenic human DNA. J. Mol. Biol. 253 (1995) 51–60.
6. Herzel, H., Grosse, I.: Correlation in DNA sequences: The role of protein coding segments. Phys. Rev. E. 55 (1997) 800–810.
7. Li, W., Kaneko, V.: DNA Correlations. Nature 360 (1992) 635–636.
8. Gelfand, M. S.: Prediction of function in DNA sequence analysis. Journal of Computational Biology 2 (1995) 87–117.
9. Gelfand, M. S., Koonin, E. V.: Avoidance of palindromic words in bacterial and archaeal genomes: A close connection with restriction enzymes. Nucl. Acid. Res 27 (1995) 2430– 2439.
10. Pedersen, A. G., Baldi, P., Chauvin, Y. Brunak, S.: The biology of eukaryotic promoter prediction. Computer and Chemistry 23 (1999) 191–207.
11. Krogh, A., Mian, I. S. Haussler, D.: A hidden Markov model that finds genes in E.Coli DNA. Nucl. Acid. Res 22 (1994) 4768–4778.
12. Liu, S. L., Lawrence, C. E.: Bayesian Inference of Biopolymer Models. Bioinformatics 15 (1999) 38–52
13. Lawrence, C. E.: Bayesian Bioinformatics. 5th international conference on intelligent systems for molecular biology, Halkidiki, Greece (1997).
14. Liu, S. L., Lawrence, C. E.: Bayesian inference of biopolymer models, Stanford Statistical Department Technical Report (1998).
15. Roman-Roldan, R., Bernaola-Galvan, P. and Oliver, J. L.: Sequence compositional complexity of DNA through an entropic segmentation method. Phys. Rev. Lett. 80 (1998) 1344.
16. Churchill, G. A.: Stochastic models for heterogeneous DNA sequences. Bull. Math. Biol. 51 (1989) 79–94.
17. Durbin, R., Eddy, Y. S., Krogh, A. Mitchison, G.: Biological Sequence Analysis. Cambridge, Cambirdge University Press (1998).
18. Muri, F., Chauveau, D., Cellier, D.: Convergence assessment in latent variable models: DNA applications. In C. P. Robert (ed.) Lectural Notes in Statistics, Vol. 135, Discretization and MCMC convergence assessment., Springer. (1998) 127–146.
19. Wolpert, D. H., Wolf, D. R.: Estimating functions of probability distributions from a finite set of samples. Phys. Rev. E. 52 (1995) 6841–6854.
20. Rozanov, Y. M.: Teoriya veroyatnosti, sluchainye processy i matematicheskaya statistika (russ: Probability Theory, Stochastic Processes and Mathematical Statisitics). Moscow, Nauka (1985).
21. Ramensky, V.E., Makeev, V.Ju., Roytberg, M.A., Tumanyan, V.G.: DNA segmentation through the bayesian approach. Journal of Computational Biology., 7 (2000), 215–231.
22. Shaeffer, G. (1999) Personal communication.
23. Finkelstein, A. V., Roytberg, M. A.: Computation of biopolymers: A general approach to different problems. BioSystems 30 (1993) 1–19.
24. Ossadnik, S.M., Buldyrev, S.V., Goldberger, A.L., Havlin, S., Mantegna, R.N., Peng, C.- K., Simons, M., Stanley, H.E.: Correlation approach to identify coding regions in DNA sequences. Biophysical Journal 67 (1994) 64–70.
25. Bernaola-Galván, P., Grosse, I., Carpena, P., Oliver, J., Román-Roldán, R., Stanley, H.: Finding borders between coding and noncoding DNA regions by an entropic segmentation method. Phys. Rev. Let., 85, (2000) 1342–1345.
26. Ono, S.: Evolution by gene duplication. Springer. (1970)