The Maximal C3 Self-Complementary Trinucleotide Circular Code X in Genes of Bacteria, Archaea, Eukaryotes, Plasmids and Viruses
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...
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doaj-e2dedb4e90714841b5cdd356847f3c5e2020-11-24T22:57:11ZengMDPI AGLife2075-17292017-04-01722010.3390/life7020020life7020020The Maximal C3 Self-Complementary Trinucleotide Circular Code X in Genes of Bacteria, Archaea, Eukaryotes, Plasmids and VirusesChristian J. Michel0Theoretical Bioinformatics, ICube, University of Strasbourg, CNRS, 300 Boulevard Sébastien Brant, 67400 Illkirch, FranceIn 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.http://www.mdpi.com/2075-1729/7/2/20circular code in genesDNA genesRNA genesdouble-stranded genessingle-stranded genes |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Christian J. Michel |
spellingShingle |
Christian J. Michel The Maximal C3 Self-Complementary Trinucleotide Circular Code X in Genes of Bacteria, Archaea, Eukaryotes, Plasmids and Viruses Life circular code in genes DNA genes RNA genes double-stranded genes single-stranded genes |
author_facet |
Christian J. Michel |
author_sort |
Christian J. Michel |
title |
The Maximal C3 Self-Complementary Trinucleotide Circular Code X in Genes of Bacteria, Archaea, Eukaryotes, Plasmids and Viruses |
title_short |
The Maximal C3 Self-Complementary Trinucleotide Circular Code X in Genes of Bacteria, Archaea, Eukaryotes, Plasmids and Viruses |
title_full |
The Maximal C3 Self-Complementary Trinucleotide Circular Code X in Genes of Bacteria, Archaea, Eukaryotes, Plasmids and Viruses |
title_fullStr |
The Maximal C3 Self-Complementary Trinucleotide Circular Code X in Genes of Bacteria, Archaea, Eukaryotes, Plasmids and Viruses |
title_full_unstemmed |
The Maximal C3 Self-Complementary Trinucleotide Circular Code X in Genes of Bacteria, Archaea, Eukaryotes, Plasmids and Viruses |
title_sort |
maximal c3 self-complementary trinucleotide circular code x in genes of bacteria, archaea, eukaryotes, plasmids and viruses |
publisher |
MDPI AG |
series |
Life |
issn |
2075-1729 |
publishDate |
2017-04-01 |
description |
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. |
topic |
circular code in genes DNA genes RNA genes double-stranded genes single-stranded genes |
url |
http://www.mdpi.com/2075-1729/7/2/20 |
work_keys_str_mv |
AT christianjmichel themaximalc3selfcomplementarytrinucleotidecircularcodexingenesofbacteriaarchaeaeukaryotesplasmidsandviruses AT christianjmichel maximalc3selfcomplementarytrinucleotidecircularcodexingenesofbacteriaarchaeaeukaryotesplasmidsandviruses |
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