Authors:
Ana Helena Tavares
1
;
Vera Afreixo
2
;
João M. O. S. Rodrigues
3
and
Carlos A. C. Bastos
3
Affiliations:
1
University of Aveiro, Portugal
;
2
University of Aveiro and Center for Research and Development in Mathematics and Applications (CIDMA), Portugal
;
3
University of Aveiro and Institute of Electronics and Telematics Engineering of Aveiro (IEETA), Portugal
Keyword(s):
Chargaff’s Second Parity Rule, Single Strand Symmetry, Oligonucleotide Distance Distribution, Human Genome.
Related
Ontology
Subjects/Areas/Topics:
Applications
;
Bioinformatics and Systems Biology
;
Pattern Recognition
;
Software Engineering
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.