Exact distribution of word counts in shuffled sequences

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.