Revision as of 12:34, 1 February 2009

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

How to use the PrimerDesigner plugin

Accessing the plugin

Selecting the target for the PCR primers

PCR primer design parameters

How to use the PrimerDesigner Plugin

How to install the PrimerDesigner plugin

First of all, you will need to Gbrowse#Installation install GBrowse, with all of its prerequisites, such as BioPerl and Graphics

Dependencies

Primer3

• Follow this link to go the primer website at Sourceforge.
• Primer3 is a binary executable, developed by Steve Rozen and colleagues, that the PrimerDesigner plugin uses to to the actual work of designing primers
• The plugin passes the DNA sequence and primer design parameters to this program and then parses the results

Installation

• Download or compile the suitable primer3 binary executable for your website.
• If necessary, change the name of the binary to 'primer3' so that it is recognized by the PrimerDesigner plugin
• The default path for primer is in '/usr/local/bin'. If you have installed it elsewhere, be sure to the the 'binpath' option (see below) in your configuration file.

Bio::PrimerDesigner

• Follow this link for information about the Bio::PrimerDesigner package.
• Bio::

Configuration

The Configuration File

Activating the Plugin

Configurable Options