Bio::PrimerDesigner::ispcr - A class for accessing the isPcr (in-silico PCR)
A low-level interface to the isPcr program. Uses supplied PCR primers, DNA
sequence and stringency parameters to predict both expected and unexpected PCR
Sets up the isPcr request for a single primer combination and returns an
If the permute flag is true, all three possible primer combinations will be
tested (ie: forward + reverse, forward + forward, reverse + reverse)
Assembles the config file and command-line arguments and sends the request to
the local binary or remote server.
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.
Defines the binary's name on the system.
There are no aliases to list for ispcr.
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.
Copyright (C) 2003-2009 Sheldon McKay <firstname.lastname@example.org<gt>,
Ken Y. Clark <email@example.com>.
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.