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

NAME

       Bio::PrimerDesigner - Design PCR Primers using primer3 and epcr

SYNOPSIS

	 use Bio::PrimerDesigner;

	 my $pd = Bio::PrimerDesigner->new;

	 #
	 # Define the DNA sequence, etc.
	 #
	 my $dna   = "CGTGC...TTCGC";
	 my $seqID = "sequence 1";

	 #
	 # Define design parameters (native primer3 syntax)
	 #
	 my %params = (
	     PRIMER_NUM_RETURN	 => 2,
	     PRIMER_SEQUENCE_ID  => $seqID,
	     SEQUENCE		 => $dna,
	     PRIMER_PRODUCT_SIZE => '500-600'
	 );

	 #
	 # Or use input aliases
	 #
	 %param = (
	     num		 => 2,
	     id 		 => $seqID,
	     seq		 => $dna,
	     sizerange		 => '500-600'
	 );

	 #
	 # Design primers
	 #
	 my $results = $pd->design( %params ) or die $pd->error;

	 #
	 # Make sure the design was successful
	 #
	 if ( !$results->left ) {
	     die "No primers found
", $results->raw_data;
	 }

	 #
	 # Get results (single primer set)
	 #
	 my $left_primer  = $results->left;
	 my $right_primer = $results->right;
	 my $left_tm	  = $results->lefttm;

	 #
	 # Get results (multiple primer sets)
	 #
	 my @left_primers  = $results->left(1..3);
	 my @right_primers = $results->right(1..3);
	 my @left_tms	   = $results->lefttm(1..3);

DESCRIPTION

       Bio::PrimerDesigner provides a low-level interface to the primer3 and epcr binary executables and supplies methods to return the results.
       Because primer3 and e-PCR are only available for Unix-like operating systems, Bio::PrimerDesigner offers the ability to accessing the
       primer3 binary via a remote server.  Local installations of primer3 or e-PCR on Unix hosts are also supported.

METHODS

   binary_path
       Gets/sets path to the primer3 binary.

   design
       Makes the primer design or e-PCR request.  Returns an Bio::PrimerDesigner::Result object.

   epcr_example
       Run test e-PCR job.  Returns an Bio::PrimerDesigner::Results object.

   list_aliases
       Lists aliases for primer3 input/output options

   list_params
       Lists input options for primer3 or epcr, depending on the context

   method
       Gets/sets method of accessing primer3 or epcr binaries.

   os_is_unix
       Returns 1 if it looks like the operating system is a Unix variant, otherwise returns 0.

   primer3_example
       Runs a sample design job for primers.  Returns an Bio::PrimerDesigner::Results object.

   program
       Gets/sets which program to use.

   run
       Alias to "design."

   url
       Gets/sets the URL for accessing the remote binaries.

   verify
       Tests local installations of primer3 or e-PCR to ensure that they are working properly.

AUTHORS

       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::primer3, Bio::PrimerDesigner::epcr.

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