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Statistical Analysis of DNA Sequence Data : a brief review

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Wybrane pełne teksty z tego czasopisma
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Warianty tytułu
Języki publikacji
EN
Abstrakty
EN
Molecular biology and the Human Genome Project generate large amounts of nucleic acid sequence data. The volume of these data makes it imperative to develop statistical techniques to detect the inner organization of DNA sequences. We review several methodologies,including M-entropies and Hidden Markov Models. A number of recent references are discussed. The existing approaches proved to be of somewhat limited usefulness, except in the domain of sequence comparison, mainly because of simplistic assumptions of the models and complicated structure of the data. Further efforts are needed to improve this situation.
Słowa kluczowe
Rocznik
Strony
171--181
Opis fizyczny
Bibliogr. 24 poz., tab., wzory
Twórcy
autor
  • Department of Statistics, Rice University, 6100 Main Street, Mail Stop 138, Houston, TX 77005, USA
Bibliografia
  • [1] B. Alberts, D. Bray, J. Lewis, M. Raff, K. Roberts and J. Watson: Molecular Biology of The Cell, Third Edition. Garland Publishing, Inc., New York, 1994.
  • [2] L. E. Baum: An inequality and associated maximization techniques in statistical estimation for probabilistic functions of Markov processes. Inequalities, 3 (1972), 1-8.
  • [3] C. Burge and S. Karlin: Finding Genes in Genomic DNA. Curr. Opin. Struct. Biol., 8 (1998), 346-354.
  • [4] C. Burge, A. Campbell and S. Karlin: Over- and under-representation of short oligonucleotides in DNA sequences. Proc. Natl. Acad. Sci., USA, 89 (1992), 1338-1362.
  • [5] S. Cebrat, M. Dudek (Eds): Statistical Physics in Biology. Physica A, 273 1-2, (1999).
  • [6] V. R. Chechetkin and A. Y. Turygin: Study of Correlations in DNA Sequences. J. theor. Biol., 178 (1996), 205-217.
  • [7] R. Durbin, S. Eddy, A. Krogh and G. Mitchison: Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge, UK, 1998.
  • [8] S. Eddy, G. Mitchison and R. Durbin: Maximum Discrimination Hidden Markov Models of Sequence Consensus. Journal of Computational Biology, 2 (1995), 9-23.
  • [9] M. Farach, M. Noordewier, S. Savari, L. Shepp, A. Wyner and J. Ziv: On the entropy of DNA: Algorithims and measurements based on memory and rapid convergence. In Proceedings of the Sixth Annual ACM-SIAM Symposium on Discrete Algorithims, January 1995.
  • [10] L. Gatlin: Information and the Living System. Columbia University Press, New York, 1972
  • [11] S. Gilbert: Developmental Biology, Fifth edition. Sinauer Associates, Inc., Sunderland, Mass., 1997.
  • [12] A. Khinchin: Mathematical Foundations of Information Theory. Dover Press, New York, 1957.
  • [13] R. Kohn: On the spectral decomposition of stationary time series using Walsh Functions I. Adv. In Appl. Prob., 12 (1980), 183-199.
  • [14] R. Kohn: On the spectral decomposition of stationary time series using Walsh Functions II. Adv. In Appl. Prob., 12 (1980), 462-474.
  • [15] L. Rabiner: A tutorial on hidden Markov models and selected applications in speech recognition. Proc. IEEE, 77 (1989), 257-285.
  • [16] A. Schmitt: Estimating the Entropy of DNA sequences. J. thoer. Biol., 1888 (1997), 369-377.
  • [17] A. Schmitt: Structural Analysis of DNA Sequences. Verlag, Dr. Koster, Berlin, 1995.
  • [18] C. E. Shannon: The Mathematical Theory of Communication. The University of Illinois Press, Urbana, Ill, 1949.
  • [19] H. E. Stanley et al.: Scaling features of non-coding DNA. Physica A, 273 1-2, (1999), 1-18.
  • [20] D. Stoffer: An introduction to Walsh-Fourier analysis and its statistical application. J of American Statistical Association, 86 (1991), 461-479.
  • [21] D. Stoffer, D. Tyler and A. Mcdougall: Spectral analysis for categorical time series: Scaling and the spectral envelope. Biometrika, 80 (1993), 611-622.
  • [22] S. Tavare and B. Giddings: Walsh transform analysis of DNA sequences. Mathematical Methods for DNA Sequences. Ed. M. Waterman. CRC Press, New York, 1989.
  • [23] A. D. Wyner, J. Wyner and J. Ziv: On the role of pattern matching in information theory. IEEE Transactions on Information Theory, 44, 6, (1998).
  • [24] A. D. Wyner, J. Wyner and J. Ziv: Information Theory: 50 Years of Discovery. Ed. Sergio Verdu and Steven McLaughlin. IEEE Press (2000), 1-12.
Typ dokumentu
Bibliografia
Identyfikator YADDA
bwmeta1.element.baztech-article-BSW9-0010-1830
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