Codon bias varies widely among the loci of Drosophila melanogaster, and some of this diversity has been explained by variation in the strength of natural selection. A study of correlations between intron and coding region base composition shows that variation in mutation pattern also contributes to codon bias variation. This finding is corroborated by an analysis of variance (ANOVA), which show...

The relationships between synonymous and nonsynonymous substitution rates and between synonymous rate and codon usage bias are important to our understanding of the roles of mutation and selection in the evolution of Drosophila genes. Previous studies used approximate estimation methods that ignore codon bias. In this study we reexamine those relationships using maximum-likelihood methods to es...

OBJECTIVE The aim was to identify the codon usage bias between the newly identified duck plague virus (DPV) UL35 gene (GenBank accession No. EF643558) and the UL35-like genes of 27 other reference herpesviruses. METHODS A comparative analysis of the codon usage bias of the 28 herpesviruses was performed by using the CodonW 1.4 program and CUSP (create a codon usage table) program of EMBOSS (T...

Most of the current codon usage bias computational approaches are only suitable for the comparison of codon usage bias within a single genome. Here we introduce a new informatics method, referred to as synonymous codon usage order (SCUO), to measure synonymous codon usage bias. In this method, we used Shannon informational theory to describe the SCUO of each gene using a value ranging from 0 to...

UNLABELLED It is well known that an amino acid can be encoded by more than one codon, called synonymous codons. The preferential use of one particular codon for coding an amino acid is referred to as codon usage bias (CUB). A quantitative analytical method, CUB and a related tool, Codon Adaptative Index have been applied to comparatively study whole genomes of a few pathogenic Trypanosomatid sp...

Codon usage biases are found in all genomes and influence protein expression levels. The codon usage effect on protein expression was thought to be mainly due to its impact on translation. Here, we show that transcription termination is an important driving force for codon usage bias in eukaryotes. Using Neurospora crassa as a model organism, we demonstrated that introduction of rare codons res...

In unicellular organisms, synonymous codon bias is correlated with the level of gene expression [1]. The codon bias becomes stronger in genes with higher expression levels. It becomes weaker but still remains in genes with lower expression levels. The bias means that synonymous codons are not used at random. In highly expressed genes, the synonymous codon usage is mainly determined by an abunda...

The phenomenon of codon usage bias has been important in the study of evolution because it provides examples of weak selection working at the molecular level. During the last two decades, evidence has accumulated that some examples of codon usage bias are driven by selection, particularly for species of fungi (e.g., Bennetzen and Hall 1982; Ikemura 1985), bacteria (e.g., Ikemura 1981; Sharp and...

In Drosophila, as in many organisms, natural selection leads to high levels of codon bias in genes that are highly expressed. Thus codon bias is an indicator of the intensity of one kind of selection that is experienced by genes and can be used to assess the impact of other genomic factors on natural selection. Among 13,000 genes in the Drosophila genome, codon bias has a slight positive, and s...