Exact distribution of word counts in shuffled sequences
Einar Andreas Rødland
Source: Adv. in Appl. Probab. Volume 38, Number 1
(2006), 116-133.
Abstract
In DNA sequences, specific words may take on biological functions as marker or signalling sequences. These may often be identified by frequent-word analyses as being particularly abundant. Accurate statistics is needed to assess the statistical significance of these word frequencies. The set of shuffled sequences - letter sequences having the same k-word composition, for some choice of k, as the sequence being analysed - is considered the most appropriate sample space for analysing word counts. However, little is known about these word counts. Here we present exact formulae for word counts in shuffled sequences.
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Keywords: Sequence shuffling; Markov chain; word count; exact distribution; hypergeometric distribution; generalised hypergeometric series; moment generating function; genome sequence analysis; directed graph; Euler path
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Permanent link to this document: http://projecteuclid.org/euclid.aap/1143936143
Digital Object Identifier: doi:10.1239/aap/1143936143
Zentralblatt MATH identifier: 05033689
Mathematical Reviews number (MathSciNet): MR2213967
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Advances in Applied Probability
