NAME

       Bio::PrimerDesigner::ispcr - A class for accessing the isPcr (in-silico PCR)  binary

SYNOPSIS

         use Bio::PrimerDesigner::ispcr;

DESCRIPTION

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

METHODS

   run
       Sets up the isPcr 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 config file and command-line arguments and sends the request to the local
       binary or remote server.

   verify
       Check to make that the isPCR binary is installed and functioning properly.  Since ispcr
       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 ispcr and an undefined
       output for some other reason.  verify uses sham ispcr 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 ispcr.

   list_params
       Returns a list of ispcr configuration options.  Required ispcr 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<gt>,
                            Ken Y. 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.