ABSTRACT
With the determination of the first gene sequences, it was noticed that alternative synonymous codons are not used in equal frequencies. Grantham and colleagues pioneered the compilation of codon usage data for many genes, allowing the description of codon usage frequency patterns, and the use of multivariate statistics to elucidate variations in these patterns. The primary reason why stop codon frequencies have not been investigated is that there is much less data—there is typically only one termination codon per gene. The relative frequencies of the several stop codons vary considerably between species. Escherichia coli was the first species in which codon usage was investigated in detail, and remains the species in which codon usage patterns are best understood. Sense codon usage in closely related species is usually very similar, and this is true for E. coli and Salmonella typhimurium.
