Dataset Information
Dicodon-based measures for modeling gene expression.
Ontology highlight
ABSTRACT: Motivation
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.Results
Through the implementation of a weighting strategy to consider the dicodon contributions, we observe that the dicodon-based measure has greater correlations with gene expression level than CAI. Interestingly, we have noted that dicodons associated with a low value of adaptiveness are related to dicodons which mediate strong translational inhibition in yeast. We have also noticed that some codon-pairs have a smaller dicodon contribution than estimated by the product of the respective codon contributions.Availability and implementation
Scripts, implemented in Python, are freely available for download at https://zenodo.org/record/7738276#.ZBIDBtLMIdU.
SUBMITTER: Alonso AM
PROVIDER: S-EPMC10287933 | biostudies-literature | 2023 Jun
REPOSITORIES: biostudies-literature
Publications
Dicodon-based measures for modeling gene expression.
Bioinformatics (Oxford, England) 20230601 6
<h4>Motivation</h4>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.<h4>Results</h4>Through the implementation of a ...[more]