Lincoln D. Stein

NAME

Bio::Graphics::Browser2::Plugin::PrimerDesigner -- a plugin to design PCR primers with primer3

SYNOPSIS

This module is not used directly

DESCRIPTION

PrimerDesigner.pm uses the Bio::PrimerDesigner API for primer3 to design PCR primers for features or target coordinates in gbrowse.

PRIMER3

Compile a primer3 (v. 0.9 or later) binary executable for your OS and copy it to the default path usr/local/bin with the name primer3. Source code for primer3 can be obtained from http://frodo.wi.mit.edu/primer3/primer3_code.html.

Designing Primers

Targeting a feature or coordinate

The target for PCR primer design is selected by clicking on an image map. For aggregate features such as gene models, etc, there is a mousover menu to select the individual part of the whole feature

Design Paramaters

The Provided set of reasonable default primer attributes will work in most cases. Product size will vary by target feature size. A suggested PCR product size range is calculated based on the selected feature. If this field is left blank, a series of increasing PCR product sizes is cycled until products big enough to flank the target feature are found. This will not necessarily find the best primers, just the first ones that produce a big enough product to flank the target. If the primers are flagged as low quality, more optimal optimal primers may be found by specifying a specific size-range.

Bio::Graphics::Browser

This plugin contains an additional package Bio::Graphics::Browser2::faux. This class inherits from Bio::Graphics::Browser. Its purpose is to keep the Bio::Graphics::Browser funtionality and configuration data while overriding image_map-related funtions required for this plugin.

TO-DO

Add support for ePCR-based scanning for false priming

FEEDBACK

See the GMOD website for information on bug submission http://www.gmod.org.

AUTHOR - Sheldon McKay

Email mckays@cshl.edi

SEE ALSO

Bio::PrimerDesigner (www.cpan.org) primer3 (http://frodo.wi.mit.edu/primer3/primer3_code.html)