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


Bio::PrimerDesigner::Result - a class for handling primer design or validation results


  use Bio::PrimerDesigner;
  # primer3  
  my $primer3_obj = Bio::PrimerDesigner->new( program => 'primer3 );  
  my $result = $primer3_obj->design( %hash_of_options );
  my $left_primer = $result->left;  
  my @left_primers = $result->left(1..$num_primers);  
  # e-PCR -- first make a hash of options from primer3 results
  # then run e-PCR
  my $epcr_obj = Bio::PrimerDesigner->new( program => 'primer3 );
  my $epcr_result = $epcr_obj->design( %hash_of_options );
  my $num_products = $epcr_result->products; 
  # one product
  my $first_prod_size = $epcr_result->size;
  my $first_prod_start = $epcr_result->start;
  my $first_prod_stop = $epcr_result->start;  
  # more than one product
  my @pcr_product_sizes = ();
  for (1..$num_products) {
      push @pcr_product_sizes, $epcr_result->size;   


 Bio::PrimerDesigner::Result will autogenerate result access methods
 for for Native Boulder IO keys and Bio::PrimerDesigner keys for
 primer3, e-PCR, isPcr and ipcress.



 This handles result method calls made via the
 Bio::PrimerDesigner::Result object.  Returns either a scalar or list
 depending on the on the arguments:

   Args passed      |  Returns
   none                scalar value for set 1
   numeric n           scalar value for set n
   numeric list 1..n   list with n elements

 The aliased output methods (below) return a string when called in a 
 scalar context and a list when called in a list context.  The native 
 primer3 (Boulder IO) keys can also be used.  There are also e-PCR,
 isPcr and ipcress specific methods

Primer3 keys

  • left -- left primer sequence
  • right -- right primer sequence
  • hyb_oligo -- internal oligo sequence
  • startleft -- left primer 5' sequence coordinate
  • startright -- right primer 5' sequence coordinate
  • tmleft -- left primer tm
  • tmright -- right primer tm
  • qual -- primer pair penalty (Q value)
  • lqual -- left primer penalty
  • rqual -- right primer penalty
  • leftgc -- left primer % gc
  • rightgc -- right primer % gc
  • lselfany -- left primer self-complementarity (any)
  • lselfend -- left primer self-complementarity (end)
  • rselfany -- right primer self-complementarity (any)
  • rselfend -- right primer self-complementarity (end)
  • pairanycomp -- primer pair complementarity (any)
  • pairendcomp -- primer pair complementarity (end)
  • lendstab -- left primer end stability
  • rendstab -- right primer end stability
  • amplicon -- amplified PCR product

Other keys

  • products -- number of PCR products
  • size -- product size
  • start -- product start coordinate
  • stop -- product stop coordinate
  • end -- synonymous with stop
  • strand -- strand of product relative to the ref. sequence (isPCR, ipcress)
  • amplicon -- returns the PCR product (isPCR only)


Copyright (c) 2003-2009 Sheldon McKay <>, Ken Youens-Clark <>.


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.


2018-07-18 perl v5.26.2