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PRIMER_DESIGNER(1p)					User Contributed Perl Documentation				       PRIMER_DESIGNER(1p)

NAME
primer_designer.pl -- command-line interface Bio::PrimerDesigner SYNOPSIS
./primer_designer.pl [options] [dna_sequence or file] Options: -p|--program Program (default "primer3") -n|--number Number of primer sets to return (default "5") -b|--binary Path to binary executable (default "/usr/local/bin") -m|--method "local" or "remote" (default "local") -u|--url URL of remote primer3/e-PCR system (default "aceserver.biotech.ubc.ca/cgi-bin/primer_designer.cgi") --list-aliases Print alias list to primer3 input options and exit --list-params Print a list of primer3/e-PCR input options and exit -h|--help Print help and exit DESCRIPTION
This script tests/demonstrates the Bio::PrimerDesigner interface to primer3 and e-PCR. It can be used with a local installation of the unix binaries or remotely via an HTTP/CGI request. AUTHOR
Copyright (C) 2003-2009 Sheldon McKay <mckays@cshl.edu>, Ken Youens-Clark <kclark@cpan.org>. SEE ALSO
Bio::PrimerDesigner. 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. perl v5.10.0 2009-08-04 PRIMER_DESIGNER(1p)

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Bio::PrimerDesigner::primer3(3pm)			User Contributed Perl Documentation			 Bio::PrimerDesigner::primer3(3pm)

NAME
Bio::PrimerDesigner::primer3 - An class for accessing primer3 SYNOPSIS
use Bio::PrimerDesigner::primer3; METHODS
Methods are called using the simplifed alias for each primer3 result or the raw primer3 BoulderIO key. Use the raw_output method to view the raw output. binary_name Defines the binary's name on the system. check_params Make sure we have required primer3 arguments. design Build the primer3 config file, run primer3, then parse the results. Expects to be passed a hash of primer3 input options. Returns an object that can be used to call result methods. request Figures out where the primer3 binary resides and accesses it with a list of parameters for designing primers. check_results Verify the validity of the design results. list_aliases Prints a list of shorthand aliases for the primer3 BoulderIO input format. The full input/ouput options and the aliases can be used interchangeably. list_params Returns a list of primer3 configuration options. primer3 will use reasonable default options for most parameters. example Runs a sample remote primer design job. Returns an Bio::PrimerDesigner::Result object. _example_dna Returns an example DNA sequence. 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::epcr. perl v5.10.0 2009-08-04 Bio::PrimerDesigner::primer3(3pm)
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