User GuidesSnapGene User Guide Agarose Gel SimulationInitiate an Agarose Gel Simulation

Initiate an Agarose Gel Simulation

How do I open and configure the Simulate Agarose Gel dialog?

Open the "Simulate Agarose Gel" Dialog

To open the Simulate Agarose Gel dialog, click Tools → Simulate Agarose Gel... .

Choose a MW Marker

Select Lane 1, and then choose a MW marker from the drop-down menu.

Select a Gel Lane

To choose a lane, click a number above the gel.

Alternatively, click the lane number in the list below the gel.

Specify the Sequence for Digestion or PCR

To specify the sequence for digestion or PCR, expand the Lane [N] menu, then choose the desired file.

View the Gel

New for SnapGene 5.2 and later: SnapGene accurately simulates relative migration rates of supercoiled (covalently closed circular) DNA.

Prior to specifying digestion with restriction enzymes, SnapGene will simulate the migration of a circular sequence as supercoiled DNA. Uncut supercoiled sequences will be marked as such in the list.

The newly added sequence will be displayed in the gel.

Optionally Specify the Gel Buffer

The migration of supercoiled DNA relative to linear DNA differs significantly depending on the electrophoresis buffer.

If you wish to change the electrophoresis buffer used for simulating the migration of supercoiled DNA, click the blue buffer indicator to open SnapGene Preferences.

Choose the new desired buffer, then close the Preferences window.