Symbolic Complexity for Nucleotide Sequences: A Sign of the Genome Structure

Abstract

We introduce a method to estimate the complexity function of symbolic dynamical systems from a finite sequence of symbols. We test such complexity estimator on several symbolic dynamical systems whose complexity functions are known exactly. We use this technique to estimate the complexity function for genomes of several organisms under the assumption that a genome is a sequence produced by a (unknown) dynamical system. We show that the genome of several organisms share the property that their complexity functions behaves exponentially for words of small length $\ell$ ($0\leq \ell \leq 10$) and linearly for word lengths in the range $11 \leq \ell \leq 50$. It is also found that the species which are phylogenetically close each other have similar complexity functions calculated from a sample of their corresponding coding regions.