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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\n", $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.
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