perlprimer(1) [debian man page]
PERLPRIMER(1) General Commands Manual PERLPRIMER(1) NAME
perlprimer - graphically specify amplicon of DNA or mRNA sequences and design primers SYNOPSIS
perlprimer DESCRIPTION
PerlPrimer calculates primer melting temperature using J. SantaLucia's extensive nearest-neighbour thermodynamic parameters. To adjust for the salt conditions of the PCR, PerlPrimer uses the empirical formula derived by von Ahsen, et al. (2001) and allows the user to specify the concentration of Mg2+, dNTPs and primers, or use standard PCR conditions. The result is a highly accurate prediction of primer melting temperature, giving rise to a maximum yeild of product when amplified. PerlPrimer is written in Perl and requires Perl/Tk. In addition, for QPCR functionality PerlPrimer requires the open-source Spidey executable from NCBI. The program is designed to be cross-platform com- patible and has been developed and tested on both Microsoft Windows and GNU/Linux-based operating systems. Users have also reported success using the program under Mac OS X. SEE ALSO
A very nice tutorial on http://perlprimer.sourceforge.net is also distributed as a debian package perlprimer-doc. AUTHOR
perlprimer was written by Owen Marshall <owenjm@users.sourceforge.net> This manual page was assembled by Steffen Moeller <steffen_moeller@gmx.de>, for the Debian project (but may be used by others). 6 January 2005 PERLPRIMER(1)
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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)