14.13 Optimize Codons

The option Optimize Codons... from the Cloning menu allows you to adapt a nucleotide sequence to the genetic code and preferred codon usage of a particular expression host. The resulting sequence is optimized to avoid use of codons that rarely occur in the highly expressed genes of the expression host, thus increasing its expression level when cloned into that species. In addition, the resulting sequence can be forced to avoid cleavage sites for a set of restriction enzymes that you specify.

This tool calculates the Codon Adaptation Index (CAI) of a gene sequence as the geometric mean of the relative adaptiveness (w) of the codons in the sequence, as defined in Sharp and Li, 1987. Relative adaptiveness is calculated from Codon Usage Tables supplied by EMBOSS, which calculate the relative codon usage of a selected set of genes in the target organism. The optimized sequence returned is the one for which CAI is maximised.

You can configure the following options (Figure 14.8 ):

After configuring your options, click OK to start the analysis and annotate the optimized codons on the sequence or create the new sequence document.


Figure 14.8: Codon Optimization options dialog.