How do I simulate an agarose gel for a PCR amplification?
Specify the Template for PCR Amplification
Click menu Tools → Simulate Agarose gel.
Set the PCR template sequence file as the input for the lane.
Choose "amplified by PCR" and Specify the PCR Primers
Choose "amplified by PCR" via the dropdown menu.
Specify the primers used to generate the PCR product by one of the following methods:
- Choose the primer name from the expanded Primer [N] menu. Tab to specify the second primer.
- Alternatively, to specify the PCR primers, click to select the first primer in Map, Sequence, or Primers view, then shift-click to select the second primer.
- Alternatively, paste each primer sequence into the 5' ... 3' boxes.
Once the primers are set, the predicted PCR product will be displayed on the gel, and the predicted fragment size will be shown in the list.
Shortcut
To quickly simulate gel electrophoresis of a PCR product do the following.
Open the template file, select the first primer, the shift click to select the second primer.
Click menu Tools → Simulate Agarose gel.
The template file will automatically be added as input to the gel.
Give the new gel a name and click ok to create the gel.
The new gel will automatically set the lane to "amplify by PCR" and use the selected primers to generate a PCR product.
