The symmetry of oligonucleotide distance distributions in the human genome

Abstract

The inter-oligonucleotide distance is defined as the distance to the next occurrence of the same oligonucleotide. In this work, using the inter-oligonucleotide distance concept, we develop new methods to evaluate the lack of homogeneity in symmetric word pairs (pairs of reversed complement oligonucleotides), in equivalent composition groups. We apply the developed methods to the human genome and we conclude that a strong similarity exists between the distance distributions of symmetric oligonucleotides. We also conclude that exceptional distance symmetry is present in several equivalent composition groups, that is, there is a strong lack of homogeneity in the group and a strong homogeneity in the included symmetric word pairs. This suggests a stronger parity rule than Chargaff’s: in the human genome, symmetric oligonucleotides have equivalent occurrence frequency and, additionally, they present similar distance distributions