Creating and editing codes is done via the Genetic Code dialog box.
At the left side of the dialog box is a chart with 64 cells representing the 64 codons. The labels on the left side of the chart are for the first nucleotide of the codon, the labels on top for the second nucleotide, and the labels on the right for the third nucleotide. Each cell of the chart contains the three-letter abbreviation of the amino acid coded for by the codon controlling that cell. To the right of the chart is a graphic that looks like a stylized tRNA anticodon loop. When you click on a cell, the codon corresponding to the selected cell will be displayed beneath the loop.
A new genetic code can be added at any time.
1. Choose Options | Modify Genetic Codes.
The Genetic Code dialog box is displayed.
2. Choose the code that will be used as a basis for the new one from the genetic code drop-down menu.
3. Type the name of the new genetic code in place of the selected code, then select the button labeled with a plus sign (+) in the upper right corner of the dialog box.
NOTE: The new code will not be saved permanently until you select OK.
4. Modify the code as required (see the procedure below).
5. Select OK to save the changes.
NOTE: The new code will become the default code, unless you select an alternative one before closing the Genetic Code dialog box.
The selected genetic code can be modified at any time. We recommend that any modifications to codes supplied with MacVector are done on a copy of the code (see the procedure above).
1. Choose Options | Modify Genetic Codes.
The Genetic Code dialog box is displayed.
2. Choose the code to be modified from the genetic code drop-down menu.
3. Select a cell whose assignment you want to change.
4. Scroll down the amino acid list on the right of the dialog box, and double-click on the amino acid you want to be coded for in the highlighted cell. If the codon does not code for an amino acid (for example, TAA, TAG, and TGA in the universal code) choose *** instead of an amino acid name.
The contents of the highlighted cell change to reflect the new assignment.
5. To designate any of the 64 codons to be a start or stop codon, select the appropriate cell, then select the start or stop button above the stylized tRNA anticodon loop.
6. Repeat steps 3 through 5 for each change you require.
6. Select OK to save the changes.
A genetic code can be deleted at any time. This should only be done with caution, because the only way you can restore it is to re-enter it by hand or to reinstall the original MacVector Library file.
1. Choose Options | Modify Genetic Codes.
The Genetic Code dialog box is displayed.
2. Choose the code to be deleted from the genetic code drop-down menu.
3. Select the button labeled with a minus sign (-) in the upper right corner of the dialog box.
4. Select OK to delete the code permanently.
NOTE: If you select Cancel, the code will not be lost, even if you have done step 3.
When you perform a reverse translation, you can eliminate codons from consideration to reduce the degeneracy of the DNA sequence that will result from the reverse translation. This can be useful, for example, when you know that your organism only uses two of the six standard serine codons in the universal genetic code.
1. Choose Options | Modify Genetic Codes.
The Genetic Code dialog box is displayed.
2. Choose the code to be modified from the genetic code drop-down menu.
3. Select a codon that you want to ignore.
4. Scroll to the end of the amino acid list on the right of the dialog box, and double click on "- - -".
5. Repeat steps 3 and 4 for each codon you want to ignore in the reverse translation.
6. Select OK to save the changes.
Each codon marked as "- - -" will not be considered when performing reverse translations.