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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

ISBN: 978-989-758-077-2

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.

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Paper citation in several formats:
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

@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},
}

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

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