Bio::PrimerDesigner

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);

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

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.