background: little knowledge of synonymous codon usage pattern of pseudorabies virus (prv) genome, especially the ul31 gene in the process for its evolution is available. objectives: in the present study, the codon usage bias between prv ul31 sequence and the ul31-like sequences was identified. materials and methods: we used a comprehensive analysis on codon usage pattern in the prv ul31 gene a...

background: most of the amino acids are encoded by more than one codon, termed as synonymous codons. synonymous codon usage is not random as it is unique to species. in each amino acid family, some synonymous codons are preferred and this is referred to as synonymous codon usage bias (scub). trends associated with evolution of scub and factors influencing its diversification in plastomes of gen...

Background: Little knowledge of synonymous codon usage pattern of pseudorabies virus (PRV) genome, especially the UL31 gene in the process for its evolution is available. Objectives: In the present study, the codon usage bias between PRV UL31 sequence and the UL31-like sequences was identified. Materials and Methods: We used a comprehensive analysi...

Background: Most of the amino acids are encoded by more than one codon, termed as synonymous codons. Synonymous codon usage is not random as it is unique to species. In each amino acid family, some synonymous codons are preferred and this is referred to as synonymous codon usage bias (SCUB). Trends associated with evolution of SCUB and factors influencing its diversification in plastomes of gen...

Non-random usage of synonymous codons, known as “codon bias”, has been described in many organisms, from bacteria to Drosophila, but little is about it phytoplankton. This phenomenon thought be driven by selection for translational efficiency. As the efficacy proportional effective population size, species with large sizes, such phytoplankton, are expected have strong codon bias. To test this, ...

χ measure. In statistics, the χ statstic computes how different the distribution of values is from a uniform distribution. Let d = c1 . . . cN be a DNA string in nucleotide alphabet, and let L be the total number of codons in d that are not Methinine or Tryptophan (the number does include the stop codons though). Let a be a k-degenerate amino acid, and let La be the total number of codons codin...

BACKGROUND In spite of extensive research on the effect of mutation and selection on codon usage, a general model of codon usage bias due to mutational bias has been lacking. Because most amino acids allow synonymous GC content changing substitutions in the third codon position, the overall GC bias of a genome or genomic region is highly correlated with GC3, a measure of third position GC conte...