Exceptional Symmetry by Genomic Word

A Statistical Analysis
  • Vera Afreixo
  • João M. O. S. Rodrigues
  • Carlos A. C. Bastos
  • Ana H. M. P. Tavares
  • Raquel M. Silva
Original Research Article


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.


Single-strand symmetry Exceptional symmetry Multiple organism comparison Genomic word analysis 



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.


  1. 1.
    Chargaff E (1950) Chemical specificity of nucleic acids and mechanism of their enzymatic degradation. Experientia 6(6):201–209CrossRefPubMedGoogle Scholar
  2. 2.
    Watson J, Crick F (1953) A structure for deoxyribose nucleic acid. Nature 171:737–738CrossRefPubMedGoogle Scholar
  3. 3.
    Karkas JD, Rudner R, Chargaff E (1968) Separation of B. subtilis DNA into complementary strands. II. Template functions and composition as determined by transcription with RNA polymerase. Proc Natl Acad Sci USA 60(3):915–920CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Rudner R, Karkas JD, Chargaff E (1968) Separation of B. subtilis DNA into complementary strands, I. Biological properties. Proc Natl Acad Sci USA 60(2):630–635CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Rudner R, Karkas JD, Chargaff E (1968) Separation of B. subtilis DNA into complementary strands. III. Direct analysis. Proc Natl Acad Sci USA 60(3):921–922CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Forsdyke DR (2011) Evolutionary bioinformatics. Springer, New YorkCrossRefGoogle Scholar
  7. 7.
    Sobottka M, Hart AG (2011) A model capturing novel strand symmetries in bacterial DNA. Biochemical and biophysical research communications 410(4):823–828. doi: 10.1016/j.bbrc.2011.06.072.
  8. 8.
    Zhang SH, Huang YZ (2008) Characteristics of oligonucleotide frequencies across genomes: conservation versus variation, strand symmetry, and evolutionary implications. Nat Precedings:1–28Google Scholar
  9. 9.
    Zhang SH, Huang YZ (2010) Strand symmetry: characteristics and origins. In: Fourth international conference on bioinformatics and biomedical engineering (iCBBE) 2010. pp. 1–4 (2010). doi: 10.1109/ICBBE.2010.5517388
  10. 10.
    Forsdyke DR, Bell SJ (2004) Purine loading, stem-loops and Chargaff’s second parity rule: a discussion of the application of elementary principles to early chemical observations. Appl Bioinform 3(1):3–8CrossRefGoogle Scholar
  11. 11.
    Baisnée PF, Hampson S, Baldi P (2002) Why are complementary DNA strands symmetric? Bioinformatics 18(8):1021–1033CrossRefPubMedGoogle Scholar
  12. 12.
    Albrecht-Buehler G (2006) Asymptotically increasing compliance of genomes with Chargaff’s second parity rules through inversions and inverted transpositions. Proc Natl Acad Sci USA 103(47):17,828–17,833CrossRefGoogle Scholar
  13. 13.
    Albrecht-Buehler G (2007) Inversions and inverted transpositions as the basis for an almost universal “format” of genome sequences. Genomics 90:297–305CrossRefPubMedGoogle Scholar
  14. 14.
    Lobry TH (1995) Properties of a general model of DNA evolution under no-strand-bias condition. J Mol Evol 40:326–330CrossRefPubMedGoogle Scholar
  15. 15.
    Hart A, Martnez S, Olmos F (2012) A gibbs approach to Chargaff’s second parity rule. J Stat Phys 146:408–422CrossRefGoogle Scholar
  16. 16.
    Powdel B, Satapathy S, Kumar A, Jha P, Buragohain A, Borah M, Ray S (2009) A study in entire chromosomes of violations of the intra-strand parity of complementary nucleotides (chargaff’s second parity rule). DNA Res 16:325–343CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Afreixo V, Rodrigues JMOS, Bastos CAC (2015) Analysis of single-strand exceptional word symmetry in the human genome: new measures. Biostatistics 16(2):209–221CrossRefPubMedGoogle Scholar
  18. 18.
    Afreixo V, Rodrigues JMOS, Bastos CAC, Silva RM (2016) Exceptional symmetry profile: A genomic word analysis. In: PACBBGoogle Scholar
  19. 19.
    Kong SG, Fan WL, Chen HD, Hsu ZT, Zhou N, Zheng B, Lee HC (2009) Inverse symmetry in complete genomes and whole-genome inverse duplication. PLoS ONE 4(11):e7553CrossRefPubMedPubMedCentralGoogle Scholar
  20. 20.
    Afreixo V, Rodrigues JMOS, Bastos CAC (2014) Exceptional single strand DNA word symmetry: analysis of evolutionary potentialities. J Integr Bioinform 11(3):250PubMedGoogle Scholar

Copyright information

© International Association of Scientists in the Interdisciplinary Areas and Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  • Vera Afreixo
    • 1
  • João M. O. S. Rodrigues
    • 2
  • Carlos A. C. Bastos
    • 2
  • Ana H. M. P. Tavares
    • 3
  • Raquel M. Silva
    • 4
  1. 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 MathematicsUniversity of AveiroAveiroPortugal
  2. 2.IEETA-Institute of Electronic Engineering and Informatics of Aveiro, Department of Electronics, Telecommunications and InformaticsUniversity of AveiroAveiroPortugal
  3. 3.iBiMED-Institute of Biomedicine, Department of MathematicsUniversity of AveiroAveiroPortugal
  4. 4.iBiMED-Institute of Biomedicine, IEETA-Institute of Electronic Engineering and Informatics of Aveiro, Department of Medical SciencesUniversity of AveiroAveiroPortugal

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