The Symmetry of Oligonucleotide Distance Distributions in the Human Genome

Ana Helena Tavares, Vera Afreixo, João M. O. S. Rodrigues, Carlos A. C. Bastos

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.

References

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Paper Citation


in Harvard Style

Tavares A., Afreixo V., M. O. S. Rodrigues J. and A. C. Bastos C. (2015). The Symmetry of Oligonucleotide Distance Distributions in the Human Genome . In Proceedings of the International Conference on Pattern Recognition Applications and Methods - Volume 2: ICPRAM, ISBN 978-989-758-077-2, pages 256-263. DOI: 10.5220/0005223102560263


in Bibtex Style

@conference{icpram15,
author={Ana Helena Tavares and Vera Afreixo and João M. O. S. Rodrigues and Carlos A. C. Bastos},
title={The Symmetry of Oligonucleotide Distance Distributions in the Human Genome},
booktitle={Proceedings of the International Conference on Pattern Recognition Applications and Methods - Volume 2: ICPRAM,},
year={2015},
pages={256-263},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0005223102560263},
isbn={978-989-758-077-2},
}


in EndNote Style

TY - CONF
JO - Proceedings of the International Conference on Pattern Recognition Applications and Methods - Volume 2: ICPRAM,
TI - The Symmetry of Oligonucleotide Distance Distributions in the Human Genome
SN - 978-989-758-077-2
AU - Tavares A.
AU - Afreixo V.
AU - M. O. S. Rodrigues J.
AU - A. C. Bastos C.
PY - 2015
SP - 256
EP - 263
DO - 10.5220/0005223102560263