bio::primerdesigner::ispcr(3pm) [debian man page]
Bio::PrimerDesigner::ispcr(3pm) User Contributed Perl Documentation Bio::PrimerDesigner::ispcr(3pm) 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. perl v5.10.0 2009-08-04 Bio::PrimerDesigner::ispcr(3pm)
Check Out this Related Man Page
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)