Trends in synonymous codon usage in adenoviruses have been examined through the multivariate statistical analysis on the annotated protein-coding regions of 22 adenoviral species, for which complete genome sequences are available. One of the major determinants of such trends is the G + C content at third codon positions of the genes, the average value of which varied from one viral genome to ot...

The phenomenon of codon usage bias is known to exist in many genomes and it is mainly determined by mutation and selection. To understand the patterns of codon usage in nemertean mitochondrial genomes, we use bioinformatic approaches to analyze the protein-coding sequences of eight nemertean species. Neutrality analysis did not find a significant correlation between GC12 and GC3. ENc-plot showe...

in order to study and compare the phosphate transporter gene codon usage and it's respond to the traits like salt tolerance, day length, pollination and temperature in different plants, 100 isoform from 10 plants are extracted from ncbi website and then analyzed with gene infinity and minitab 16 software. the result shows that the highest codon usage similarity (81.95%) was for wheat and oryza ...

BACKGROUND AND PURPOSE Codon and amino acid usage biases determined in numerous organisms have deciphered the architectures of their protein-coding genes to some extent. To understand the architecture of protein-coding genes of Aeromonas phages, codon and amino acid usage biases have been investigated in the protein-coding genes of the Aeromonas hydrophila phage Aeh1. METHODS In order to stud...

The relationship between gene length and synonymous codon usage bias was investigated in Drosophila melanogaster, Escherichia coli and Saccharomyces cerevisiae. Simulation studies indicate that the correlations observed in the three organisms are unlikely to be due to sampling errors or any potential bias in the methods used to measure codon usage bias. The correlation was significantly positiv...

Current models of codon substitution are formulated at the levels of nucleotide substitution and do not explicitly consider the separate effects of mutation and selection. They are thus incapable of inferring whether mutation or selection is responsible for evolution at silent sites. Here we implement a few population genetics models of codon substitution that explicitly consider mutation bias ...

Codons that code for the same amino acid are often used with unequal frequencies. This phenomenon is termed codon bias. Here, we report a computational analysis of codon bias in yeast using experimental and theoretical genome-wide data. We show that the most used codons in highly expressed genes can be predicted by mRNA structural data and that the codon choice at each synonymous site within an...

Codon bias is the non-random use of synonymous codons, a phenomenon that has been observed in species as diverse as bacteria, plants and mammals. The preferential use of particular synonymous codons may reflect neutral mechanisms (e.g. mutational bias, G|C-biased gene conversion, genetic drift) and/or selection for mRNA stability, translational efficiency and accuracy. The extent to which these...

The genetic code is degenerate--most amino acids can be encoded by from two to as many as six different codons. The synonymous codons are not used with equal frequency: not only are some codons favored over others, but also their usage can vary significantly from species to species and between different genes in the same organism. Known causes of codon bias include differences in mutation rates...

Synonymous mutations are ‘‘silent’’ with regard to the amino acid sequence of a protein, but a wealth of evidence indicates that, at least in species with large effective population sizes, synonymous mutations are subject to translational selection (Akashi and EyreWalker 1998). One line of evidence for translational selection has been the perceived negative correlation between codon bias and sy...