GANT provides a graphical interface to the primer picking software, Primer3, developed by the Whitehead Institute for Biomedical Research.
Start by selecting the region of the gene which you would like to span with primers. Once you have selected a region, you may start the primer picking process one of two ways:
Click "Pick Primers..." from the "Primers" menu as shown here:
- OR -
Right click (or Ctrl+click) the selected region and click "Span with Primers..." as shown here:
Both of these methods will open the primer picking dialog shown here:
Click "Generate Primers" to span the selected region with primer pairs using the default settings.
Alternatively, you may alter the default settings such as the Minimum Overlap between primer pairs or any of the options in the drop-down list:
By selecting one of the options in the drop-down list, the option will automatically be displayed along with the default value as shown here:
You may alter the default value or uncheck the option which will make it disappear once again. A description of the options can be found here: http://frodo.wi.mit.edu/primer3/README.primer3_1.0.0
The Minimum Overlap option is the minimum overlap of the right primer of one primer pair and the left primer of the next primer pair (default: 0).
Once you have decided on the primer picking options and clicked "Generate Primers", the primer pairs will appear as dumbbell-shaped objects in the annotation area of each gene view. You can see the primer pairs in both the Transcript View and Genomic View as shown here (circled):
Here is an up-close view after zooming in to the 5th exon:
To get details on one or more primer pairs, select the primer pairs, right click (or Ctrl+click) the primer pairs, and click "Get Details...". An Annotation Details window will appear with all the details of the primer pair which can be used to order the primer pair(s) from an oligo synthesis company.
Primer picking is packaged with free primer picking for a limited time. After that, the primer picking capabilities may be enabled by purchasing a code from Bio::Neos, Inc. Pricing is available at http://bioneos.com/products/gant/.
If you attempt to design primers a see a window appear like the following:
Then your code has expired and you may contact Bio::Neos, Inc. to purchase a new one. Once you have received the code, select "About" from the "Help" menu:
You will see an window appear like the following:
Simply enter your 16-digit code at the bottom and click "Ok" for your code to be saved. You may then continue designing oligos.
Once you have designed oligos, you may save them to a file using the export wizard. Simply choose "Export Primers..." from the "Primers" menu:
You will then see the following "Export Primers" window:
Change the options if you desire and then click "Save to file..." to export your primers to a file. Options include how to delimiter the fields in the file, whether or not to include column headers, and which fields to include. You may also change the order of the fields by using the "Up" and "Down" buttons. You will see an example of the output file at the bottom.
To help you organize your primers, you may mark individual primer pairs as "Succeeded", "Failed", or "Unknown". Simply select the primer pairs you wish to mark and then choose the status from "Primers" > "Mark Selected Primers As". The color of the primer pairs will change to reflect their status.
You may also rename primer pairs by selecting a single primer pair and then choose "Rename Selected Primer" from the "Primers" menu.
To delete primers you have picked, choose "Clear Unsaved Primers..." from the "Primers" menu:
