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Exceptional Single Strand DNA Word Symmetry: Universal Law?

  • Vera Afreixo
  • João M. O. S. Rodrigues
  • Carlos A. C. Bastos
Part of the Advances in Intelligent Systems and Computing book series (AISC, volume 294)

Abstract

Some previous studies point to the extension of Chargaff’s second rule (the phenomenon of symmetry) to words of large length. However, in random sequences generated by an independent symbol model where the probability of occurrence of complementary nucleotides is the same, we expect that the phenomenon of symmetry holds for all word lengths. In this work, we measure the symmetry above that expected in independence contexts (exceptional symmetry), for several organisms: viruses; archaea; bacteria; eukaryotes. The results for each organism were compared to those obtained in control scenarios. We created a new organism genomic signature consisting of a vector of the measures of exceptional symmetry for words of lengths 1 through 12. We show that the proposed signature is able to capture essential relationships between organisms.

Keywords

DNA Single strand symmetry Exceptional symmetry Effect size measure 

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Copyright information

© Springer International Publishing Switzerland 2014

Authors and Affiliations

  • Vera Afreixo
    • 1
  • João M. O. S. Rodrigues
    • 2
  • Carlos A. C. Bastos
    • 2
  1. 1.CIDMA - Center for Research and Development in Mathematics and Applications, Department of MathematicsUniversity of AveiroAveiroPortugal
  2. 2.Signal Processing Lab., IEETA and Department of Electronics Telecommunications and InformaticsUniversity of AveiroAveiroPortugal

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