Proper functioning of biological cells requires that the process of protein expression be
carried out with high efficiency and fidelity. Given an amino‐acid sequence of a protein …

The frequencies of alternative synonymous codons vary both among species and among
genes from the same genome. These patterns have been inferred to reflect the action of …

The codon composition of the coding sequence's (ORF) 5′ end first few dozen codons is
known to be distinct to that of the rest of the ORF. Various explanations for the unusual …

Viruses differ markedly in their specificity toward host organisms. Here, we test the level of
general sequence adaptation that viruses display toward their hosts. We compiled a …

The ratio of non-synonymous to synonymous substitutions (dN/dS) is a useful measure of
the strength and mode of natural selection acting on protein-coding genes. It is widely used …

Although translational selection to favour codons that match the most abundant tRNAs is not
readily observed in humans, there is nonetheless selection in humans on synonymous …

Upstream open reading frames (uORFs) play widespread regulatory functions in modulating
mRNA translation in eukaryotes, but the principles underlying the genomic distribution and …

Background It is widely acknowledged that synonymous codons are used unevenly among
genes in a genome. In organisms under translational selection, genes encoding highly …

Background While effective population size (N e) and life history traits such as generation
time are known to impact substitution rates, their potential effects on base composition …

Whether codon usage fine-tunes mRNA translation in mammals remains controversial, with
recent papers suggesting that production of proteins in specific Gene Ontological (GO) …