Numerical comparison of several approximations of the word count distribution in random sequences.
The exact distribution of word counts in random sequences and several approximations have been proposed in the past few years. The exact distribution has no theoretical limit but may require prohibitive computation time. On the other hand, approximate distributions can be rapidly calculated but, in practice, are only accurate under specific conditions. After making a survey of these distributions, we compare them according to both their accuracy and computational cost. Rules are suggested for choosing between Gaussian approximations, compound Poisson approximation, and exact distribution. This work is illustrated with the detection of exceptional words in the phage Lambda genome.
Robin
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INRA, Unité Mathématique, Informatique & Génome, F78026 Versailles, France. Stephane.Robin@versailles.inra.fr
Schbath
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D010582:Bacteriophage lambda / Q000235:genetics; D001483:Base Sequence; D019295:Computational Biology; D004279:DNA, Viral / Q000235:genetics; D016679:Genome, Viral; D008037:Linguistics; D008390:Markov Chains; D016012:Poisson Distribution
D004279:DNA, Viral