PrimerDesigner is a GBrowse plugin, written by Sheldon McKay, that uses use the primer3 program to design PCR primers for selected regions within the genome browser. Please feel free to contact the author or The Gbrowse mailing list for help or more information.

The video below demonstrates designing PCR primers using the PrimerDesigner plugin.


How to use the PrimerDesigner plugin

Accessing the plugin

Reports and Analysis.png

PrimerDesigner Front.png

Zoom pan.png

Selecting the target for the PCR primers

Target Highlight.png

Target Selected.png

PCR primer design parameters

PCR Params.png

Predicted PCR Primer Results

PCR Results.png

Note On Quality Scores

Uh oh.png

How to install the PrimerDesigner plugin

First of all, you will need to install GBrowse, with all of its prerequisites, such as BioPerl and Bio::Graphics



Installing Primer3


Installing Bio::PrimerDesigner


The Configuration File

Activating the Plugin

To activate the Primer Designer plugin, simple add its name to the list of available plugins in the configuration file for you data source.

For example:

# Installed plugins
plugins = Spectrogram SequenceDumper PrimerDesigner

NOTE: For this plugin to work properly, you must ensure that all dependencies (described above) are that the GBrowse database has DNA sequence.

Configurable Options

To configure the plugin, add a stanza like this at the end of your [GENERAL] section:

binpath = /usr/bin/
method  = local
ispcr   =

The default value is ‘/usr/local/bin’

Use this option to specify where the primer3 binary is located, if not in the default ‘/usr/local/bin’

If you are using a remote URL (primer3 is installed on another server), specify a URL instead.

The default value is ‘local’

Recognized options are ‘local’ (primer3 installed on the same server as Gbrowse) or remote (primer3 is installed on another server).

The ‘remote’ method is implicit if the binpath option is set to a URL beginning with


default size
The default value is 10_000

This option specifies the default segment size to show in the PrimerDesigner image

max range
The default value is 300

This option species the degree to which the PCR product size can depart from the optimal size, as determined by the size of the selected target area for PCR primers.

This option can be set to a URL that point to the UCSC in silico PCR sight.

If selected, in silico PCR results will be reported in the output of this plugin

These results help to determine if the correct amplicon is found and also indicate whether other PCR products

are amplified by the primer pair.

You must check the site to see if there is a genome sequence for you species and modify the above example accordingly

PrimerDesigner and GBrowse 2

The PrimerDesigner plugin does not work with GBrowse 2.00. Work is currently underway to fix this before the next release of GBrowse.