Bio::PrimerDesigner::primer3(3pm)			User Contributed Perl Documentation			 Bio::PrimerDesigner::primer3(3pm)

NAME

       Bio::PrimerDesigner::primer3 - An class for accessing primer3

SYNOPSIS

	 use Bio::PrimerDesigner::primer3;

METHODS

       Methods are called using the simplifed alias for each primer3 result or the raw primer3 BoulderIO key.  Use the raw_output method to view
       the raw output.

   binary_name
       Defines the binary's name on the system.

   check_params
       Make sure we have required primer3 arguments.

   design
       Build the primer3 config file, run primer3, then parse the results.  Expects to be passed a hash of primer3 input options.  Returns an
       object that can be used to call result methods.

   request
       Figures out where the primer3 binary resides and accesses it with a list of parameters for designing primers.

   check_results
       Verify the validity of the design results.

   list_aliases
       Prints a list of shorthand aliases for the primer3 BoulderIO input format.  The full input/ouput options and the aliases can be used
       interchangeably.

   list_params
       Returns a list of primer3 configuration options.  primer3 will use reasonable default options for most parameters.

   example
       Runs a sample remote primer design job.	Returns an Bio::PrimerDesigner::Result object.

   _example_dna
       Returns an example DNA sequence.

AUTHOR

       Copyright (C) 2003-2009 Sheldon McKay <mckays@cshl.edu>, Ken Youens-Clark <kclark@cpan.org>.

LICENSE

       This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by
       the Free Software Foundation; version 3 or any later version.

       This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of
       MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more details.

       You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation,
       Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.

SEE ALSO

       Bio::PrimerDesigner::epcr.

perl v5.10.0							    2009-08-04					 Bio::PrimerDesigner::primer3(3pm)