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Life 2017, 7(2), 20; doi:10.3390/life7020020

The Maximal C3 Self-Complementary Trinucleotide Circular Code X in Genes of Bacteria, Archaea, Eukaryotes, Plasmids and Viruses

Theoretical Bioinformatics, ICube, University of Strasbourg, CNRS, 300 Boulevard Sébastien Brant, 67400 Illkirch, France
Academic Editor: David Deamer
Received: 6 February 2017 / Revised: 23 March 2017 / Accepted: 31 March 2017 / Published: 18 April 2017
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Abstract

In 1996, a set X of 20 trinucleotides was identified in genes of both prokaryotes and eukaryotes which has on average the highest occurrence in reading frame compared to its two shifted frames. Furthermore, this set X has an interesting mathematical property as X is a maximal C 3 self-complementary trinucleotide circular code. In 2015, by quantifying the inspection approach used in 1996, the circular code X was confirmed in the genes of bacteria and eukaryotes and was also identified in the genes of plasmids and viruses. The method was based on the preferential occurrence of trinucleotides among the three frames at the gene population level. We extend here this definition at the gene level. This new statistical approach considers all the genes, i.e., of large and small lengths, with the same weight for searching the circular code X . As a consequence, the concept of circular code, in particular the reading frame retrieval, is directly associated to each gene. At the gene level, the circular code X is strengthened in the genes of bacteria, eukaryotes, plasmids, and viruses, and is now also identified in the genes of archaea. The genes of mitochondria and chloroplasts contain a subset of the circular code X . Finally, by studying viral genes, the circular code X was found in DNA genomes, RNA genomes, double-stranded genomes, and single-stranded genomes. View Full-Text
Keywords: circular code in genes; DNA genes; RNA genes; double-stranded genes; single-stranded genes circular code in genes; DNA genes; RNA genes; double-stranded genes; single-stranded genes
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Michel, C.J. The Maximal C3 Self-Complementary Trinucleotide Circular Code X in Genes of Bacteria, Archaea, Eukaryotes, Plasmids and Viruses. Life 2017, 7, 20.

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