codon usagethe frequency with which a particular organism uses the available CODONS in genes. The majority of AMINO ACIDS are coded for by more than one codon (see GENETIC CODE and there are marked preferences for the use of the alternative codons amongst different species. For example, in bacteria CCG is the preferred codon for the amino acid proline, rather than CCU, CCC or CCA. Codon usage can affect the efficiency of translation, particularly when cloned heterologous genes are being expressed. If the cloned gene contains a large number of unfavoured codons the tRNA molecules of the host may not effectively recognize them, so reducing translation and hence the amount of protein synthesized.
ORF SCANNING takes codon usage into account to facilitate the location of genes, since real EXONS are likely to display a bias for certain codons, whereas runs of chance triplets will not. Codon usage is also called codon bias.