PrimerDesigner.pm

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PrimerDesigner.png

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.

How to use the PrimerDesigner plugin

Accessing the plugin

From GBrowse main page, the PrimerDesigner plugin, as well as other installed plugins, can be accessed via the 'Reports and Analysis' menu.

File:Reports and Analysis

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 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

Installing Primer3

  • 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::PrimerDesigner is a set of perl modules that provide a low-level API for the primer3 program.
  • Note: Bio::PrimerDesigner is not part of BioPerl or GBrowse; you will have to install this package for the Primerdesigner plugin to work.

Installing Bio::PrimerDesigner

  • Bio::PrimerDesigner is on CPAN (the Comprehensive Perl Archive Network).
  • To install it, you can use the CPAN shell.

Configuration

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 GFFDumper 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

binpath
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.
method
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 'http://'
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.