bio::primerdesigner::primer3(3pm) [debian man page]
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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Bio::PrimerDesigner::epcr(3pm) User Contributed Perl Documentation Bio::PrimerDesigner::epcr(3pm) 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. perl v5.10.0 2009-08-04 Bio::PrimerDesigner::epcr(3pm)