/ 
Bio-PrimerDesigner-0.04
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/ Bio::PrimerDesigner::ispcr

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) 2003-2008 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 2.

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., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA.

SEE ALSO

Bio::PrimerDesigner::primer3.