Codon Usage Enhancer (CUE): A JAVA-based Freeware for

Manipulating Codon Usage


Nancy Yu*, Yi-Sheng Cheng

Bioinformatics-Biology Service Core, Institute of Molecular Biology, Academia Sinica, Nan-Kang, Taipei 11529, Taiwan University, Taiwan

No.128 Academia Road Section 2, Nan-Kang, Taipei, 11529, Taiwan


Within an organism, for codons that are more common in the genome, especially the ones in the highly expressed genes, there tends to be more copies of corresponding tRNAs. Codons that occur less frequently in the genome have lower numbers of corresponding tRNA species; this influences the efficiency and accuracy of translation for these codons. Hence, if one has difficulty in expressing a gene in a foreign host organism, one of the problems could be differences with respect to codon preference. The Codon Usage Enhancer is a program created to help identify and deal with this problem. The tool gives a visual overview of an input gene’s codon weights relative to the reference host organism.  Based on a tabulated list of optimal codons for the host organism, the program suggests the best substitution for codons whose relative weights fall below a certain threshold.  For Escherichia coli, the program also identifies all codon pairs within the input sequence that do not normally appear in the genome, as this may also contribute to decrease in translation efficiency.  In addition, the software allows users to further modify the gene sequence according to their needs, while keeping track of the nucleotides that are modified in the process as well as the weights of the codons that result from user modifications.  The output analysis of the program can be easily exported and saved as distinct files for convenience.