A Quick Overview of the Gibthon Construct Designer (GCD)

As you can see, we've made a few changes to the GCD.

Here's a quick walkthrough of how to use the new version and a few hints as to what's in the works.

1) Import the required fragments into gibthon

Fragments can be imported from various sources including NCBI entrez and a number of file formats in the `fragment' app.

2) Crop the fragments to the region of interest

Fragments can be cropped in the fragment view, in the `fragment' app.

We're currently developing a way of selecting regions within fragments from the gibthon app itself. This would eliminate the need for this step and the extra fragments it generates. See this issue.

3) Drag and Drop

Drag and drop the fragments into their correct order in the Construct Designer. Adding a fragment to the inner position inserts it in the reverse direction.

4) Confirm settings

Enter the settings for the reaction(s) in the settings tab

5) Process

Click process to design your primers

6) Download Protocols and View Warnings

Warnings are displayed whenever gibthon detects a potential problem with your primers. Often these warnings will not affect the outcome of the reaction, but judgement is required as to the severity of the problem.

We're working on a method for manually adjusting the length of the primers in order to avoid warnings as well as a general improvement of the way these primers are displayed. Being able to see that your primers are sane at a glance is a key design goal. See this issue.