Codon usage preference patterns have been associated with modulation of translation efficiency, protein folding, and mRNA decay. However, new studies support that codon pair usage has also a remarkable effect at the gene expression level. Here, we expand the concept of CAI to answer if codon pair usage patterns can be understood in terms of codon usage bias, or if they offer new information regarding coding translation efficiency
The authors found that the dicodon-based measure has a stronger connection with gene expression level than CAI after employing a weighting technique to take the contributions of the dicodon into account.The authors have discovered an intriguing relationship between dicodons that cause substantial translational inhibition in yeast and dicodons associated with a low value of adaptiveness. Additionally, we have seen that the product of the individual codon contributions overestimates the dicodon contribution of several codon-pairs.
The python scripts are available at the following URL:https://zenodo.org/record/7738276#.ZBIDBtLMIdU.
Reference:
Diambra L. et. al.(2023) Dicodon-based measures for modeling gene expression. Bioinformatics 39(6): btad 380