Distances between dinucleotides in the human genome

Abstract

We developed a methodology to process DNA sequences based on the inter-dinucleotide distances and we characterized the inter-dinucleotide distance distributions of the human genome. The distance distribution of each dinucleotide was compared to the distance distribution of all the other dinucleotides using the Kullback-Leibler divergence. We found out that the divergence between the distribution of the distances of a dinucleotide and that of its reversed complement is very small, indicating that these distance distributions are very similar. This is an interesting finding that might give evidence of a stronger parity rule than the one provided by Chargaff's second parity rule. Furthermore, we also compared the distance distribution of each dinucleotide to a reference distribution, that of a random sequence generated with the same dinucleotide abundances, revealing the CG dinucleotide as the one with the highest cumulative relative error for the first 60 distances. © 2011 Springer-Verlag Berlin Heidelberg.