Over- and underrepresentation of short DNA words in herpesvirus genomes

The relative abundance and rarity of DNA words have been recognized in previous biological studies to have implications for the regulation, repair, and evolutionary mechanisms of a genome. In this paper, we review several different measures of abundance and rarity of DNA words, including z-scores, representation ratios, and cross-ratios, that have appeared in the recent literature, and examine the concordance among them using the human cytomegalovirus genome sequence. We then rank all words of length k = 2, ..., 5 of seven herpesvirus genomes according to their abundance, as measured by one of the z-scores based upon a stationary Markov model of order k-2. Using a simple metric on the ranks of 2-words of the seven herpesvirus sequences, we construct an evolutionary tree. Several 3-words are observed to be consistently over- or underrepresented in all seven herpesviruses. Furthermore, clusters of some of the most over- and underrepresented 4- and 5-words in the genomes are identified with functional sites such as the origins of replication and regulatory signals of individual viruses.