Figure 4.

Translation efficiency selective enhancement, describing one hill climbing iteration of the translation optimization algorithm. The first step is to define the wanted and un-wanted hosts. The second step is to calculate the CUB score of each organism for all codons of amino acid $A$ to $Ai$ ($scor{e}_{Ai}$) and then calculate the mean (${\mathsf{\mu }}_{\mathrm{CUBi}}$) and the standard deviation (${\mathsf{\sigma }}_{\mathrm{CUBi}})$ of the CUB scores. Finally, an optimization score is calculated for each synonymous codon. All the amino acid codons in the initial sequence are switched to the codon with the maximal optimization score as calculated.