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Exceptional Symmetry by Genomic Word

A Statistical Analysis

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Abstract

Single-strand DNA symmetry is pointed as a universal law observed in the genomes from all living organisms. It is a somewhat broadly defined concept, which has been refined into some more specific measurable effects. Here we discuss the exceptional symmetry effect. Exceptional symmetry is the symmetry effect beyond that expected in independence contexts, and it can be measured for each word, for each equivalent composition group, or globally, combining the effects of all possible words of a given length. Global exceptional symmetry was found in several species, but there are genomic words with no exceptional symmetry effect, whereas others show a very high exceptional symmetry effect. In this work, we discuss a measure to evaluate the exceptional symmetry effect by symmetric word pair, and compare it with others. We present a detailed study of the exceptional symmetry by symmetric pairs and take the CG content into account. We also introduce and discuss the exceptional symmetry profile for the DNA of each organism, and we perform a multiple comparison for 31 genomes: 7 viruses; 5 archaea; 5 bacteria; 14 eukaryotes.

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Acknowledgements

This work was supported by Portuguese funds through the iBiMED-Institute of Biomedicine, IEETA-Institute of Electronics and Informatics Engineering of Aveiro, CIDMA - Center for Research and Development in Mathematics and Applications and the Portuguese Foundation for Science and Technology (“FCT–Fundação para a Ciência e a Tecnologia”), within projects: UID/BIM/04501/2013, PEst-OE/EEI/UI0127/2014 and UID/MAT/04106/2013.

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Authors and Affiliations

  1. iBiMED-Institute of Biomedicine, IEETA-Institute of Electronic Engineering and Informatics of Aveiro, CIDMA- Center for Research and Development in Mathematics and Applications, Department of Mathematics, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal

    Vera Afreixo

  2. IEETA-Institute of Electronic Engineering and Informatics of Aveiro, Department of Electronics, Telecommunications and Informatics, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal

    João M. O. S. Rodrigues & Carlos A. C. Bastos

  3. iBiMED-Institute of Biomedicine, Department of Mathematics, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal

    Ana H. M. P. Tavares

  4. iBiMED-Institute of Biomedicine, IEETA-Institute of Electronic Engineering and Informatics of Aveiro, Department of Medical Sciences, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal

    Raquel M. Silva

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  1. Vera Afreixo
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  2. João M. O. S. Rodrigues
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  3. Carlos A. C. Bastos
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  4. Ana H. M. P. Tavares
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  5. Raquel M. Silva
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Correspondence to Vera Afreixo.

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Afreixo, V., Rodrigues, J.M.O.S., Bastos, C.A.C. et al. Exceptional Symmetry by Genomic Word. Interdiscip Sci Comput Life Sci 9, 14–23 (2017). https://doi.org/10.1007/s12539-016-0200-9

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  • DOI: https://doi.org/10.1007/s12539-016-0200-9

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