NAME Bio::PrimerDesigner - Design PCR Primers using primer3 and epcr SYNOPSIS use Bio::PrimerDesigner; my $pd = Bio::PrimerDesigner->new; # # Define the DNA sequence, etc. # my $dna = "CGTGC...TTCGC"; my $seqID = "sequence 1"; # # Define design parameters (native primer3 syntax) # my %params = ( PRIMER_NUM_RETURN => 2, PRIMER_SEQUENCE_ID => $seqID, SEQUENCE => $dna, PRIMER_PRODUCT_SIZE => '500-600' ); # # Or use input aliases # %param = ( num => 2, id => $seqID, seq => $dna, sizerange => '500-600' ); # # Design primers # my $results = $pd->design( %params ) or die $pd->error; # # Make sure the design was successful # if ( !$results->left ) { die "No primers found\n", $results->raw_data; } # # Get results (single primer set) # my $left_primer = $results->left; my $right_primer = $results->right; my $left_tm = $results->lefttm; # # Get results (multiple primer sets) # my @left_primers = $results->left(1..3); my @right_primers = $results->right(1..3); my @left_tms = $results->lefttm(1..3); DESCRIPTION Bio::PrimerDesigner provides a low-level interface to the primer3 and epcr binary executables and supplies methods to return the results. Because primer3 and e-PCR are only available for Unix-like operating systems, Bio::PrimerDesigner offers the ability to accessing the primer3 binary via a remote server. Local installations of primer3 or e-PCR on Unix hosts are also supported. METHODS binary_path Gets/sets path to the primer3 binary. design Makes the primer design or e-PCR request. Returns an Bio::PrimerDesigner::Result object. epcr_example Run test e-PCR job. Returns an Bio::PrimerDesigner::Results object. list_aliases Lists aliases for primer3 input/output options list_params Lists input options for primer3 or epcr, depending on the context method Gets/sets method of accessing primer3 or epcr binaries. os_is_unix Returns 1 if it looks like the operating system is a Unix variant, otherwise returns 0. primer3_example Runs a sample design job for primers. Returns an Bio::PrimerDesigner::Results object. program Gets/sets which program to use. run Alias to "design." url Gets/sets the URL for accessing the remote binaries. verify Tests local installations of primer3 or e-PCR to ensure that they are working properly. AUTHORS Copyright (C) 2003-2009 Sheldon McKay , Ken Youens-Clark . 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, Bio::PrimerDesigner::epcr.