NAME

       Bio::PrimerDesigner::epcr - A class for accessing the epcr binary

SYNOPSIS

         use Bio::PrimerDesigner::epcr;

DESCRIPTION

       A low-level interface to the e-PCR binary.  Uses supplied PCR primers, DNA sequence and
       stringency parameters to predict both expected and unexpected PCR products.

METHODS

   run
       Sets up the e-PCR request for a single primer combination and returns an
       Bio::PrimerDesigner::Result object

       If the permute flag is true, all three possible primer combinations will be tested (ie:
       forward + reverse, forward + forward, reverse + reverse)

   request
       Assembles the e-PCR config file and command-line arguments and send the e-PCR request to
       the local e-PCR binary or remote server.

   verify
       Check to make that the e-PCR binary is installed and functioning properly.  Since e-PCR
       returns nothing if no PCR product is found in the sequence, we have to be able to
       distinguish between a valid, undefined output from a functioning e-PCR and an undefined
       output for some other reason.  verify uses sham e-PCR data that is known to produce a PCR
       product.

   binary_name
       Defines the binary's name on the system.

   list_aliases
       There are no aliases to list for epcr.

   list_params
       Returns a list of e-PCR configuration options.  Required e-PCR input is a sequence string
       or file and the left and right primers.  Default values will be used for the remaining
       options if none are supplied.

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::primer3.