Difference between revisions of "PrimerDesigner.pm"
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* Primer3 is a binary executable, developed by Steve Rozen and colleagues, that the PrimerDesigner plugin uses to to the actual work of designing primers | * 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 | * The plugin passes the DNA sequence and primer design parameters to this program and then parses the results | ||
| − | ==== | + | ====Installing Primer3==== |
* [http://sourceforge.net/project/showfiles.php?group_id=112461&package_id=211061&release_id=595603 Download or compile] the suitable primer3 binary executable for your website. | * [http://sourceforge.net/project/showfiles.php?group_id=112461&package_id=211061&release_id=595603 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 | * If necessary, change the name of the binary to 'primer3' so that it is recognized by the PrimerDesigner plugin | ||
Revision as of 12:48, 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]
Contents
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
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.
- Bio::PrimerDesigner is not installed with 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 comprehensice perl archive network).
- To install it, you can use the CPAN shell.
Configuration
The Configuration File
Activating the Plugin
Configurable Options
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