Numerical Solutions for Patterns Statistics on Markov Chains
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Nuel Gregory: Laboratoire Statistique et Genome, CNRS (8071), INRA (1152), UEVE, Evry, France
Statistical Applications in Genetics and Molecular Biology, 2006, vol. 5, issue 1, 1-45
We propose here a review of the methods available to compute pattern statistics on text generated by a Markov source. Theoretical, but also numerical aspects are detailed for a wide range of techniques (exact, Gaussian, large deviations, binomial and compound Poisson). The SPatt package (Statistics for Pattern, free software available at http://stat.genopole.cnrs.fr/spatt) implementing all these methods is then used to compare all these approaches in terms of computational time and reliability in the most complete pattern statistics benchmark available at the present time.
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