Codon Harmonizer

Codon Harmonizer is an online tool for the adaptation of genes to be used for heterologous protein expression. In contrast to codon optimization, the process of harmonization can be considered as a milder one. For some cases it can be advantageous that rare codons are not substituted by codons with high frequencies. Rare codons may function as regulators and give the protein time to fold through a different folding pathway to enhance correct folding and solubility. Codon harmonization can be seen as an alternative to the conventional “black box” codon optimization procedure and might help in solubilisation of the heterologously expressed proteins. The Codon Harmonizer is using the STANDARD CODON USAGE as used for example in E. coli. If you are using sequences from organisms having a different codon usage you must adapt these codons manually.

Choose a method for codon harmonization:

The frequency of each codon is calculated in the set of all codons, independently from their corresponding amino acid. The frequencies of all codons will sum up to 100%.

The frequencies of the codons encoding a single amino acid are calculated separately. So every amino acid has codons with frequencies summing up to 100%.

For detailed information regarding methods and the program we refer to "PAPER".

Input data:

The number in squared brackets at the end of the organism's name tells you how many genes were used to create the codon usage table by

Select if you do not want the codons in the output sequence to be separated by spaces.

Please cite: "Horst Lechner, to be published"