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.IX Title "Bio::PrimerDesigner::epcr 3pm"
.TH Bio::PrimerDesigner::epcr 3pm "2013-09-03" "perl v5.18.1" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
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.SH "NAME"
Bio::PrimerDesigner::epcr \- A class for accessing the epcr binary
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Bio::PrimerDesigner::epcr;
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
A low-level interface to the e\-PCR binary.  Uses supplied \s-1PCR\s0 primers,
\&\s-1DNA\s0 sequence and stringency parameters to predict both expected 
and unexpected \s-1PCR\s0 products.
.SH "METHODS"
.IX Header "METHODS"
.SS "run"
.IX Subsection "run"
Sets up the e\-PCR request for a single primer combination and returns 
an Bio::PrimerDesigner::Result object
.PP
If the permute flag is true, all three possible primer combinations 
will be tested (ie: forward + reverse, forward + forward, reverse + reverse)
.SS "request"
.IX Subsection "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.
.SS "verify"
.IX Subsection "verify"
Check to make that the e\-PCR binary is installed and functioning
properly.  Since e\-PCR returns nothing if no \s-1PCR\s0 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 \s-1PCR\s0 product.
.SS "binary_name"
.IX Subsection "binary_name"
Defines the binary's name on the system.
.SS "list_aliases"
.IX Subsection "list_aliases"
There are no aliases to list for epcr.
.SS "list_params"
.IX Subsection "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.
.SH "AUTHOR"
.IX Header "AUTHOR"
Copyright (C) 2003\-2009 Sheldon McKay <mckays@cshl.edu>,
Ken Youens-Clark <kclark@cpan.org>.
.SH "LICENSE"
.IX Header "LICENSE"
This program is free software; you can redistribute it and/or modify
it under the terms of the \s-1GNU\s0 General Public License as published by
the Free Software Foundation; version 3 or any later version.
.PP
This program is distributed in the hope that it will be useful, but
\&\s-1WITHOUT ANY WARRANTY\s0; without even the implied warranty of
\&\s-1MERCHANTABILITY\s0 or \s-1FITNESS FOR A PARTICULAR PURPOSE. \s0 See the \s-1GNU\s0
General Public License for more details.
.PP
You should have received a copy of the \s-1GNU\s0 General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, \s-1MA 02110\-1301
USA.  \s0
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::PrimerDesigner::primer3.