Brachypodium distachyon has been proposed as a new model for the temperate grass because it is related to the major cereal grain species (such as wheat, barley, oat, maize, rice, and sorghum) and many forage and turf species. In this study, a multivariate statistical analysis was performed to investigate the characteristics of codon bias and the main factors affecting synonymous codon usag...

A comparative analysis of the codon usage bias in the newly discovered dUTPase gene (Assigned Accession No.: DQ486149) of the duck enteritis virus (DEV) and the dUTPase gene of 32 reference herpesviruses was performed. The results indicated that the DEV dUTPase gene encodes a protein of 477 amino acids, which includes five conserved motifs with a 3–1–2–4–5 arrangement. The codon adaptation inde...

Like other species of Drosophila, Drosophila pseudoobscura has a distinct bias toward the usage of C- and G-ending codons. Previous studies have indicated that this bias is due, at least in part, to natural selection. Codon bias clearly differs among amino acids (and other codon classes) in Drosophila, which may reflect differences in the intensity of selection on codon usage. Ongoing natural s...

Species-speci c diversity of genes in codon-usage is fundamentally important characteristic for determining suitability of genes in genomes and estimating protein-production levels of genes. We have developed measures which re ect diversity of genes in codon usage by means of a multivariate statistical method and assess species-speci c diversity of genes in codon usage for four organisms, Bacil...

UNLABELLED INteractive Codon usage Analysis (INCA) provides an array of features useful in analysis of synonymous codon usage in whole genomes. In addition to computing codon frequencies and several usage indices, such as 'codon bias', effective Nc and CAI, the primary strength of INCA has numerous options for the interactive graphical display of calculated values, thus allowing visual detectio...

Codon usage biases are found in all eukaryotic and prokaryotic genomes and have been proposed to regulate different aspects of translation process. Codon optimality has been shown to regulate translation elongation speed in fungal systems, but its effect on translation elongation speed in animal systems is not clear. In this study, we used a Drosophila cell-free translation system to directly c...

Adaptive codon usage provides evidence of natural selection in one of its most subtle forms: a fitness benefit of one synonymous codon relative to another. Codon usage bias is evident in the coding sequences of a broad array of taxa, reflecting selection for translational efficiency and/or accuracy as well as mutational biases. Here, we quantify the magnitude of selection acting on alternative ...