You may alter a currently selected code by using the Project > Edit Genetic Codes menu command.
Caution: Changes to Genetic Codes made in in this application will affect other Lasergene applications.
You can modify codon assignments and the degeneracy for a back translated amino acid. You can assign the altered code a new name by typing it into the Description text box. You must have entered at least one sequence before editing a genetic code.
1) Choose the desired code by selecting Project > Genetic Codes, and then continue by clicking Project > Edit Genetic Code. The Genetic Code Editor will appear:
2) To modify codon assignments, including stop codons, use your mouse to drag the codon to the appropriate amino acid row. The color of the codon will change from red to black to show it has been moved. Only red codons are considered during aggregate codon calculation for the set.
3) If you would like to include the newly moved codon when calculating the aggregate codon, use Alt/Option+click (Win/Mac) on the codon to change it back to red. The sum of all codons in the row will then be recalculated to give the revised reverse translation codon. The same recalculation occurs instantly when a codon is removed from a row. Reverse translation codons, shown in the third column from the left, are the codons used when reverse translating a protein sequence.
4) To change the codons used for back translation without changing the forward translation, use Alt/Option+click (Win/Mac) on codons you want to exclude.
5) For example, in the Standard Genetic Code, there are two codons for Cysteine (UGU and UGC) and the default reverse translation codon is UGY (Y means pyrimidine, i.e. C or U). If you want all Cysteine residues to be reverse translated to UGC, Alt/Option+click (Win/Mac) on the UGU codon to change its color to black so it is not considered for reverse translation. The reverse translation codon for Cysteine will now read UGC instead of UGY.
6) To edit start codons, click Set Starts tab. A second screen will appear.
Select the desired start codons visually by finding the row containing the first base (on the left), following that over to the column belonging to the second base (in the center) and selecting the row in the table that aligns with the third base (on the right).
Clicking the desired amino acid causes it to turn green, and an asterisk to appear next to it.
The codon representing the amino acid is shown at the top of the screen to the right of the word STARTS.
Up to eleven start codons may be selected.
To remove a start codon from the list you have created at the top of the page, click on the corresponding amino acid in the body of the table.
7) Click To RNA/To DNA in either screen to toggle T's and U's.
8) When you are finished, close the Genetic Code Editor window. If you have made changes, a dialog will prompt you to save them. Click Save As to close the Edit dialog and open a Save dialog. Type a name for the modified code, find a location in which to store the code document, and click Save.