Abstract
Oligonucleotide array hybridization allows one to read a DNA sequence by interpreting the pattern generated when the sequence hybridizes to an array of known oligonucleotides. Because of noise and cross-hybridization, there is uncertainty about the frequency of occurrence of each oligonucleotide in the sequence, and it is necessary to set up a model relating sequences to the data sets they are expected to generate. This model has parameters specifying the noise level and the pattern of cross-hybridization; we use the maximum entropy algorithm MemSys5 to estimate cross-hybridization parameters from data sets corresponding to known sequences, and to choose between different models. To determine an unknown sequence from a data set, a maximum entropy reconstruction provides estimates of the noise level and the frequency of occurrence of each oligonucleotide. This information allows candidate sequences to be evaluated against the data and probabilities to be assigned to them.
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References
Kristensen, T., Lopez, R. and Prydz, H: 1992, An estimate of the sequencing error frequency in the DNA sequence databases’, DNA Sequence 2: 343–346.
Churchill, G.A. and Waterman, M.S.: 1992, The accuracy of DNA sequences: estimating sequence quality’, Genomics 14(1): 89–98.
Bains, W. and Smith, G.C.: 1988, A novel method for nucleic acid sequence determination’, Journal of Theoretical Biology 135 (3): 303–307.
Bains, W.:1991, Hybridization methods for DNA sequencing’, Genomics 11(2): 294–301.
Pevzner, P.A.: 1989, l-tuple DNA sequencing: computer analysis’, Journal of Biomolecular Structure and Dynamics 7(1): 63–73.
Garrett, A.J.M.: 1991, Ockham’s razor’, in Maximum Entropy and Bayesian Methods, Laramie, 1990, W.T. Grandy and L.J. Schicke (eds.), pp. 357–364. Dordrecht: Kluwer.
Gull, S.F. and Skilling, J.:1991, Quantified Maximum Entropy MemSys5 Users’ Manual. Royston: Maximum Entropy Data Consultants. Version 1. 01.
Gull, S.F.: 1989, Developments in maximum entropy data analysis’, in Maximum Entropy and Bayesian Methods, Cambridge, 1988, J. Skilling (ed.), pp. 53–71. Dordrecht: Kluwer.
Skilling, J.:1989, Classic maximum entropy’, in Maximum Entropy and Bayesian Methods, Cambridge, 1988,J. Skilling (ed.), pages 45–52. Dordrecht: Kluwer.
Southern, E.M., Maskos, U. and Elder, J.K.: 1992, Analyzing and comparing nucleic acid sequences by hybridization to arrays of oligonucleotides: evaluation using experimental models’, Genomics 13 (4): 1008–1017.
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© 1993 Springer Science+Business Media Dordrecht
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Elder, J.K. (1993). Analysis of DNA Oligonucleotide Hybridization Data by Maximum Entropy. In: Mohammad-Djafari, A., Demoment, G. (eds) Maximum Entropy and Bayesian Methods. Fundamental Theories of Physics, vol 53. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-2217-9_44
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DOI: https://doi.org/10.1007/978-94-017-2217-9_44
Publisher Name: Springer, Dordrecht
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