codon usage

codon usage

the 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.

References in periodicals archive ?
vittatus and further compared their genome structure and organization, nucleotide variation and codon usage. We also reported the phylogenetic analysis using protein sequences from P.
Nucleotide composition, codon usage, and relative synonymous codon usage (RSCU) were determined with MEGA v6.0 (Kumar et al.
Codon usage bias (CUB) and RNA secondary structures (RSS) were analyzed for salt stress responsive (SSR) genes of Arabidopsis thaliana and Solanum lycopersicum.
The topics include emerging and re-emerging enterically transmitted hepatitis viruses, Hepatitis A virus codon usage: implications for translation kinetics and capsid folding, nonhuman primate models of Hepatitis A and Hepatitis E infections, the transmission and epidemiology of Hepatitis E virus genotype three and four infections, innate and adaptive immunity, and immunization.
Synonymous codon usage in Bacillus subtilis reflects both translational selection and mutational biases.
Berkhout, "Impact of the biased nucleotide composition of viral RNA genomes on RNA structure and codon usage," Journal of General Virology, vol.
The watermark should be embedded into coding DNA by considering codon degeneracy, to preserve the protein sequence, and codon optimization, including codon usage and GC content [10,11].
subtilis main codons based on Codon Usage Database (Kazusa DNA Research Institute, Japan; Website: http:// www.kazusa.or.jp/codon), To reduce the potential toxic effects of expressed AMPs on B.
MetaGUN [11] implements a three-stage strategy to predict genes by firstly classifying input sequence into different phylogenetic groups, then identifying genes for each group independently with support vector machine (SVM) classifier that integrate entropy density profile of codon usage, translation initiation site scores, and ORF length as the input features, and finally adjusting TISs by employing a modified version of MetaTISA.
The codons of the gene must also be optimized for the organism due to codon usage bias.
In a similar vein, Hart (this volume) argues that HTS transcriptomic studies produce sufficient data to explore the interface of theoretical population genetic models (e.g., isolation-with-migration) and codon usage models.