Insert Codons into a Sequence

How do I add codons to an existing coding sequence?

Open a DNA Sequence File and Define the Insertion Point

Open a DNA sequence and switch to Sequence view.

Click at the position you wish to insert codons, with consideration of the CDS read frame, or select 1 or more nucleotides if you wish to replace a region with one or more codons.

Open the "Insert Codon" Tool

Click menu Edit → Insert → Codons....

Choose the Codons to Add to the Sequence

Set the "Genetic code" and "Codon Usage Table" (optional) for the intended host of your new synthetic sequence.

Use the Drop-down list to choose the amino acid encoded by the codon codon.

Choose a Synonymous Codon to Add

Use the drop-down list to choose a synonymous codon. If you have specified a codon usage table, then the "Preferred" (most commonly used) codon will be marked. Any codons regarded as rare will also be marked as such.

You can also choose codons with ambiguous positions that specify multiple synonymous codons. Note that if the codon is markeds as "Ambiguous", then it will encode multiple amino acid types.

With the desired codon selected, click Insert to set the first codon.

Add Further Codons

If required, select and add further codons.

If you are adding codons to a CDS that runs in the reverse orientation then check the option to "reverse complement" to add the reverse complement of all codons.

If you wish to change a synonymous codon after addition, then click on the amino acid name to select an alternative codon.

Once the desired codons are chosen, click Replace to add the new codons to your sequence.

Confirm the New Codons

In Sequence view, click "Show Colors" in the side toolbar to highlight the newly added codons.

Save the file, or click menu File → Save As to save the modified file as a new file.

If you wish to add multiple sequence elements to an existing sequence then consider using the Design Synthetic Sequence tool