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PRIMER_DESIGNER(1p)					User Contributed Perl Documentation				       PRIMER_DESIGNER(1p)

NAME
primer_designer.pl -- command-line interface Bio::PrimerDesigner SYNOPSIS
./primer_designer.pl [options] [dna_sequence or file] Options: -p|--program Program (default "primer3") -n|--number Number of primer sets to return (default "5") -b|--binary Path to binary executable (default "/usr/local/bin") -m|--method "local" or "remote" (default "local") -u|--url URL of remote primer3/e-PCR system (default "aceserver.biotech.ubc.ca/cgi-bin/primer_designer.cgi") --list-aliases Print alias list to primer3 input options and exit --list-params Print a list of primer3/e-PCR input options and exit -h|--help Print help and exit DESCRIPTION
This script tests/demonstrates the Bio::PrimerDesigner interface to primer3 and e-PCR. It can be used with a local installation of the unix binaries or remotely via an HTTP/CGI request. AUTHOR
Copyright (C) 2003-2009 Sheldon McKay <mckays@cshl.edu>, Ken Youens-Clark <kclark@cpan.org>. SEE ALSO
Bio::PrimerDesigner. 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. perl v5.10.0 2009-08-04 PRIMER_DESIGNER(1p)

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Bio::PrimerDesigner::Result(3pm)			User Contributed Perl Documentation			  Bio::PrimerDesigner::Result(3pm)

NAME
Bio::PrimerDesigner::Result - a class for handling primer design or validation results SYNOPSIS
use Bio::PrimerDesigner; # # primer3 # my $primer3_obj = Bio::PrimerDesigner->new( program => 'primer3 ); my $result = $primer3_obj->design( %hash_of_options ); my $left_primer = $result->left; my @left_primers = $result->left(1..$num_primers); # # e-PCR -- first make a hash of options from primer3 results # then run e-PCR # my $epcr_obj = Bio::PrimerDesigner->new( program => 'primer3 ); my $epcr_result = $epcr_obj->design( %hash_of_options ); my $num_products = $epcr_result->products; # # one product # my $first_prod_size = $epcr_result->size; my $first_prod_start = $epcr_result->start; my $first_prod_stop = $epcr_result->start; # # more than one product # my @pcr_product_sizes = (); for (1..$num_products) { push @pcr_product_sizes, $epcr_result->size; } DESCRIPTION
Bio::PrimerDesigner::Result will autogenerate result access methods for for Native Boulder IO keys and Bio::PrimerDesigner keys for primer3, e-PCR, isPcr and ipcress. METHODS
keys This handles result method calls made via the Bio::PrimerDesigner::Result object. Returns either a scalar or list depending on the on the arguments: ------------------+------------------------ Args passed | Returns ------------------+------------------------ none scalar value for set 1 numeric n scalar value for set n numeric list 1..n list with n elements The aliased output methods (below) return a string when called in a scalar context and a list when called in a list context. The native primer3 (Boulder IO) keys can also be used. There are also e-PCR, isPcr and ipcress specific methods Primer3 keys o left -- left primer sequence o right -- right primer sequence o hyb_oligo -- internal oligo sequence o startleft -- left primer 5' sequence coordinate o startright -- right primer 5' sequence coordinate o tmleft -- left primer tm o tmright -- right primer tm o qual -- primer pair penalty (Q value) o lqual -- left primer penalty o rqual -- right primer penalty o leftgc -- left primer % gc o rightgc -- right primer % gc o lselfany -- left primer self-complementarity (any) o lselfend -- left primer self-complementarity (end) o rselfany -- right primer self-complementarity (any) o rselfend -- right primer self-complementarity (end) o pairanycomp -- primer pair complementarity (any) o pairendcomp -- primer pair complementarity (end) o lendstab -- left primer end stability o rendstab -- right primer end stability o amplicon -- amplified PCR product Other keys o products -- number of PCR products o size -- product size o start -- product start coordinate o stop -- product stop coordinate o end -- synonymous with stop o strand -- strand of product relative to the ref. sequence (isPCR, ipcress) o amplicon -- returns the PCR product (isPCR only) 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. perl v5.10.0 2009-08-04 Bio::PrimerDesigner::Result(3pm)
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