Exceptional Single Strand DNA Word Symmetry: Universal Law?
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.
KeywordsDNA Single strand symmetry Exceptional symmetry Effect size measure
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- 2.Afreixo, V., Garcia, S.P., Rodrigues, J.M.O.S.: The breakdown of symmetry in word pairs in 1,092 human genomes. Jurnal Teknologi 66(3), 1–8 (2013)Google Scholar
- 5.Forsdyke, D.R.: Evolutionary Bioinformatics. Springer, Berlin (2010)Google Scholar
- 6.Forsdyke, D.R., Bell, S.J.: Purine loading, stem-loops and Chargaff’s second parity rule: a discussion of the application of elementary principles to early chemical observations. Applied Bioinformatics 3(1), 3–8 (2004)Google Scholar
- 7.Karkas, J.D., Rudner, R., Chargaff, E.: Separation of B. subtilis DNA into complementary strands. II. template functions and composition as determined by transcription with RNA polymerase. Proceedings of the National Academy of Sciences of the United States of America 60(3), 915–920 (1968)CrossRefGoogle Scholar
- 8.Kong, S.-G., Fan, W.-L., Chen, H.-D., Hsu, Z.-T., Zhou, N., Zheng, B., Lee, H.-C.: Inverse symmetry in complete genomes and whole-genome inverse duplication. PLoS One 4(11), e7553 (2009)Google Scholar
- 15.Zhang, S.-H., Huang, Y.-Z.: Strand symmetry: Characteristics and origins. In: 2010 4th International Conference on Bioinformatics and Biomedical Engineering (iCBBE), pp. 1–4 (June 2010)Google Scholar