An Application of Information Theoretical Measures for DNA Structure

Objective: This study makes use of the application of entropy in information theory in the DNA structure. We applied the information theoretic notion of entropy and Kullback-Leibler distance to characterize the distribution of exons, introns and amino acid in DNA sequences. Material and Methods: Entropy, relative entropy and mutual information values for exons, introns and amino acid are computed based on their probability distribution. An application to perform a comparison exon / intron and amino acid sequences in some human genome is briefly discussed. Results: The two major divisions of an Eukaryotes DNA that are transcribed into RNA are protein-coding sections called exons, and nonprotein-coding sections called introns. It makes good intuitive sense that introns and exons probability distributions may be different, since they are subject to different random process. Although, introns are usually more highly diversified than neighboring exons, we obtain that the probability distribution of exons and introns are similar. In analyzing the splice site regions of exons and introns, it is observed that the probability distributions of the bases are very different than the probability distributions of all the bases of exons and introns. Conclusion: The entropy of a number of DNA coding and non-coding sequences collected from different genomes was calculated for finite sequences. A distance measure was applied to compare exon and intron information content and it was found that they are structurally quite similar. Although, introns are usually more highly diversified than neighboring exons, we obtain that the probability distribution of exons and introns are similar. This unforeseen result exhibits that introns can carry nearly as much information as exons. In analyzing the splice site regions of exons and introns, it is observed that the probability distributions of the bases are very different than the probability distributions of all the bases of exons and introns. We may claim that one may obtain information on the splice site region of the genes by examining the probability distributions of the last bases of exons before the GT pair and the first bases of introns after the GT pair.