Primer Designer Robot

This page describes the use of the Primer Designer Robot. If you would like to know how the algorithm works internally please click here.

The motivation to write the Primer Designer robot came directly from the Freiburg Bioware team. In one of the many casual meetings at the lab they told us, that a common mistake in Synthetic Biology is designing the wrong primers for PCR and thus wasting a lot of money and time. Since designing a primer is an easily automated process, we decided to develop this robot and include it into our project.

How to design a primer

This is the parameters menu of the Primer Designer Robot.

If you want to design a set of primers please select the sequence from the workspace that you want to amplify using PCR. If you have more than one or no sequence at all selected the Primer Designer will not work.
Now click the "Design Primer" Button in the Primer Designer's menu. You will see the menu as shown in the image above. In this menu you can select the desired melting temperature for the primers. If you want to you can also specify a start and endpoint in the target sequence. By default the robot will design a primer for the whole sequence.
Once you're done with the settings click "send".
The robot will now design the primers and display them like this:

If you are satisfied with the result, you can store both primers in the workspace, so you can export them. To do so just click the "Store in Workspace" Button. To make it easy to identify them there you can specify custom names for them first.

Brief Overview of Algorithm

Once activated the Primer Design first evaluates the input form and loads the sequence from the workspace.
The first primer is then assembled following these steps:
The robot adds one base after until the following restrictions are matched:

• Primer length must be at least 18 Bases
• Primer melting temperature must be close to the specified goal temperature
• Primer must end with G or C

The temperatures are calculated using the formulas given on Oligocalc.
After the first primer is found the second primer is calculated the same, but with the first primers melting temperature as target. Then the robot displays the output and spawn the gadget that allows the user to specify the names and send the primers to the workspace. After the button is clicked the robot stores the primers in the workspace.