The species in which you wish to express the harmonised gene.
The species from which the DNA you are harmonising is obtained from.
The tool expects the nucleotide sequence to start from the first codon of the encoded protein.
It does not expect DNA from upstream of the coding region. Do not be tempted to include the promoter region as well as the coding region.
The input sequence should be a DNA sequence - It does not expect RNA sequences.
The input sequence should be for coding regions only and so the number of nucleotides inputted should be divisible by 3. If the gene you want to express contains introns then take the mature mRNA sequence and convert that to the corresponding DNA sequence and then submit that DNA sequence to this tool.
Insert the minimum codon usage percentage of the target organism which you would like to use.
This is important because there are instances where a codon is extremely infrequently used in a species and so if it is selected it may cause expression problems even if that codon has the closest usage percentage to the source organism.
For example: If the source organism uses `ATT` 3% of the time to encode Isoleucine and the target organism uses `ATC` 0.1% of the time to encode isoleucine then if there is no threshold set the tool would choose `ATC` for expression in the target. This would be potentially problematic as a codon usage of 0.1% may cause very low levels of expression.
To circumvent this problem a threshold of 1 would mean that `ATC` would not be chosen because 0.1% < 1%.
The tool expects for the final codon in the input sequence to be a stop codon. If it is then it chooses the most commonly used stop codon in the target species.
If the final codon is not a stop codon then it is treated as an ordinary codon and a stop codon will not be chosen.
The algorithm always converts the first codon of the input sequence into the `ATG` start codon.
If you have any comments or experience problems then contact us at tools@forgegenetics.com