Genes are clustered by using factorial correspondence analysis into three classes. Class I contains genes involved in most metabolic processes. Class II genes correspond to genes highly and continuously expressed during exponential growth. Class III genes are implicated in horizontal transfer of DNA.
The Codon Adaptation Tool (JCAT) presents a simple method to adapt the Codon Usage to most sequenced prokaryotic organisms and selected eukaryotic organisms. The codon adaptation plays a major role in cases where foreign genes are expressed in hosts and the codon usage of the host differs from that of the organism where the gene stems from.
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