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.