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.
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  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
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