Kleffe J, Borodovsky M
Department of Molecular Biology and Informatics, Free University of Berlin, Germany.
Comput Appl Biosci. 1992 Oct;8(5):433-41. doi: 10.1093/bioinformatics/8.5.433.
An exact expression for the variance of random frequency that a given word has in text generated by a Markov chain is presented. The result is applied to periodic Markov chains, which describe the protein-coding DNA sequences better than simple Markov chains. A new solution to the problem of word overlap is proposed. It was found that the expected frequency and overlapping properties determine most of the variance. The expectation and variance of counts for triplets are compared with experimental counts in Escherichia coli coding sequences.
