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OLIGOTM(1)						       Primer3 User Manuals							OLIGOTM(1)

NAME
oligotm - Prints oligo's melting temperature on stdout SYNOPSIS
oligotm [OPTIONS] {oligo} where oligo is a DNA sequence of between 2 and 36 bases DESCRIPTION
oligotm prints the melting temperature of a given desoxyribooligonucleotide on the standard output. It is part of the oligotm library. OPTIONS
-mv monovalent_conc Concentration of monovalent cations in mM, by default 50 mM. -dv divalent_conc Concentration of divalent cations in mM, by default 0 mM. -n dNTP_conc Concentration of deoxynycleotide triphosphate in mM, by default 0 mM. -d dna_conc Concentration of DNA strands in nM, by default 50 nM. -tp [0|1] Specifies the table of thermodynamic parameters and the method of melting temperature calculation: o 0 Breslauer et al., 1986 and Rychlik et al., 1990 (used by primer3 up to and including release 1.1.0). This is the default, but not the recommended value. o 1 Use nearest neighbor parameter from SantaLucia 1998. This is the recommended value. -sc [0..2] Specifies salt correction formula for the melting temperature calculation: o 0 Schildkraut and Lifson 1965, used by primer3 up to and including release 1.1.0. This is the default, but not the recommended value. o 1 SantaLucia 1998. This is the recommended value. o 1 Owczarzy et al., 2004. -i prints references to publications which were used for thermodynamic calculations. REFERENCE
Please cite Rozen, S., Skaletsky, H. "Primer3 on the WWW for general users and for biologist programmers." In S. Krawetz and S. Misener, eds. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology. Humana Press, Totowa, NJ, 2000, pages 365-386. SEE ALSO
primer3_core(1) ntdpal(1) COPYRIGHT
Copyright (C) 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008 Whitehead Institute for Biomedical Research, Steve Rozen (http://jura.wi.mit.edu/rozen), Helen Skaletsky All rights reserved. On Debian-based systems, please consult /usr/share/doc/primer3/copyright to read the licence of oligotm. This manual page was written by Charles Plessy <plessy@debian.org> for the Debian(TM) system (but may be used by others). Permission is granted to copy, distribute and/or modify this document under the same terms as oligotm itself. oligotm 1.1.4 05/09/2008 OLIGOTM(1)

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Bio::PrimerDesigner::primer3(3pm)			User Contributed Perl Documentation			 Bio::PrimerDesigner::primer3(3pm)

NAME
Bio::PrimerDesigner::primer3 - An class for accessing primer3 SYNOPSIS
use Bio::PrimerDesigner::primer3; METHODS
Methods are called using the simplifed alias for each primer3 result or the raw primer3 BoulderIO key. Use the raw_output method to view the raw output. binary_name Defines the binary's name on the system. check_params Make sure we have required primer3 arguments. design Build the primer3 config file, run primer3, then parse the results. Expects to be passed a hash of primer3 input options. Returns an object that can be used to call result methods. request Figures out where the primer3 binary resides and accesses it with a list of parameters for designing primers. check_results Verify the validity of the design results. list_aliases Prints a list of shorthand aliases for the primer3 BoulderIO input format. The full input/ouput options and the aliases can be used interchangeably. list_params Returns a list of primer3 configuration options. primer3 will use reasonable default options for most parameters. example Runs a sample remote primer design job. Returns an Bio::PrimerDesigner::Result object. _example_dna Returns an example DNA sequence. 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::epcr. perl v5.10.0 2009-08-04 Bio::PrimerDesigner::primer3(3pm)
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