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Exceptional single strand DNA word symmetry: analysis of evolutionary potentialities

Afreixo, Vera ; Rodrigues, João M.O.S. ; Bastos, Carlos A.C.

Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)


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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. We also create 27 control scenarios with the same length of each genome under study. 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.


Institution: Faculty of Technology, Research Groups in Informatics
DDC classification: Data processing, computer science, computer systems

Suggested Citation:
Afreixo, Vera ; Rodrigues, João M.O.S. ; Bastos, Carlos A.C.  (2014)  Exceptional single strand DNA word symmetry: analysis of evolutionary potentialities. Journal of Integrative Bioinformatics - JIB (ISSN 1613-4516)

Online-Journal: http://journal.imbio.de/article.php?aid=250
URL: http://biecoll.ub.uni-bielefeld.de/volltexte/2014/5341



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