Correlation matrix for quartet codon usage

TL;DR

This paper investigates the correlation matrix of codon usage in vertebrates, demonstrating that certain sum rules hold across species and supporting these findings with entropy measures and observed suppression patterns.

Contribution

It introduces a theoretical correlation matrix based on sum rules for codon usage and validates it against experimental data from 26 vertebrate species.

Findings

The correlation matrix aligns well with experimental data.

Sum rules for codon usage are largely species-independent.

Suppression of CG and AU dinucleotides is observed.

Abstract

It has been argued that the sum of usage probabilities for codons, belonging to quartets, that have as third nucleotide C or A, is independent of the biological species for vertebrates. The comparison between the theoretical correlation matrix derived from these sum rules and the experimentally computed matrix for 26 species shows a satisfactory agreement. The Shannon entropy, weakly depending on the biological species, gives further support. Suppression of codons containing the dinucleotides CG or AU is put in evidence.