Correlations in Usage Frequencies and Shannon Entropy for Codons

TL;DR

This study analyzes codon usage frequencies and Shannon entropy across 92 species, revealing correlations that support the crystal basis model of the genetic code, with weak species dependence.

Contribution

It uncovers specific correlations in codon usage and entropy that align with the crystal basis model, providing new insights into genetic code structure.

Findings

Correlations between usage frequencies of synonymous codons with third nucleotide A and C.

Weak dependence of Shannon entropy on species.

Observed correlations fit the crystal basis model.

Abstract

The usage frequencies for codons belonging to quartets are analized, over the whole exonic region, for 92 biological species. Correlation is put into evidence, between the usage frequencies of synonymous codons with third nucleotide A and C and between the usage frequencies of non synonymous codons, belonging to suitable subsets of the quartets, with the same third nucleotide. A correlation is pointed out between amino acids belonging to subsets of the set encoded by quartets of codons. It is remarked that the computed Shannon entropy for quartets is weakly dependent on the biological species. The observed correlations well fit in the mathematical scheme of the crystal basis model of the genetic code.