An overview on the distribution of word counts
in Markov chains


J. Comp. Biol. 7, 2000.


In this paper, we give an overview about the different results existing on the statistical distribution of word counts in a Markovian sequence of letters. Results concerning the number of overlapping occurrences, the number of renewals and the number of clumps will be presented. Counts of single words but also multiple words are considered. Most of the results are approximations as the length of the sequence tends to infinity. We will see that Gaussian approximations switch to (compound) Poisson approximations for rare words. Modeling DNA sequences or proteins by stationary Markov chains, these results can be used to study the statistical frequency of motifs in a given sequence.

Key words and phrases word count distribution, Markovian random sequence, overlapping occurrences, renewals, clumps.

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