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author Petar Petrov <slackalaxy@gmail.com>2018-07-08 19:42:08 +0100
committer David Spencer <idlemoor@slackbuilds.org>2018-07-08 19:42:08 +0100
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treea85f77e8f01018ab9be721d1348b073ace28eba1 /academic/primer3/man1/oligotm.1
parent5c821121ece759ad907abbdf81c640c805eb197d (diff)
downloadslackbuilds-4ce886af277886c629ab55efeb23b07874369c00.tar.gz
slackbuilds-4ce886af277886c629ab55efeb23b07874369c00.tar.xz
academic/primer3: Updated for version 2.4.0.
Signed-off-by: David Spencer <idlemoor@slackbuilds.org>
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+'\" t
+.\" Title: OLIGOTM
+.\" Author: [FIXME: author] [see http://docbook.sf.net/el/author]
+.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
+.\" Date: 11/30/2011
+.\" Manual: Primer3 User Manuals
+.\" Source: oligotm 1.1.4
+.\" Language: English
+.\"
+.TH "OLIGOTM" "1" "11/30/2011" "oligotm 1.1.4" "Primer3 User Manuals"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+oligotm \- Prints oligo\*(Aqs melting temperature on stdout
+.SH "SYNOPSIS"
+.HP \w'\fBoligotm\fR\ 'u
+\fBoligotm\fR [OPTIONS] {oligo}
+.PP
+where oligo is a DNA sequence of between 2 and 36 bases
+.SH "DESCRIPTION"
+.PP
+
+\fBoligotm\fR
+prints the melting temperature of a given deoxyribonucleotide on the standard output\&. It is part of the oligotm library\&.
+.SH "OPTIONS"
+.PP
+\fB\-mv\fR \fImonovalent_conc\fR
+.RS 4
+Concentration of monovalent cations in mM, by default 50\ \&mM\&.
+.RE
+.PP
+\fB\-dv\fR \fIdivalent_conc\fR
+.RS 4
+Concentration of divalent cations in mM, by default 0\ \&mM\&.
+.RE
+.PP
+\fB\-n\fR \fIdNTP_conc\fR
+.RS 4
+Concentration of deoxynucleotide triphosphate in mM, by default 0\ \&mM\&.
+.RE
+.PP
+\fB\-d\fR \fIdna_conc\fR
+.RS 4
+Concentration of DNA strands in nM, by default 50\ \&nM\&.
+.RE
+.PP
+\fB\-tp\fR \fI[0|1]\fR
+.RS 4
+Specifies the table of thermodynamic parameters and the method of melting temperature calculation:
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+\fI0\fR
+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
+\fInot\fR
+the recommended value\&.
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+\fI1\fR
+Use nearest neighbor parameter from SantaLucia 1998\&.
+\fIThis is the recommended value\fR\&.
+.RE
+.RE
+.PP
+\fB\-sc\fR \fI[0\&.\&.2]\fR
+.RS 4
+Specifies salt correction formula for the melting temperature calculation:
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+\fI0\fR
+Schildkraut and Lifson 1965, used by primer3 up to and including release 1\&.1\&.0\&. This is the default, but
+\fInot\fR
+the recommended value\&.
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+\fI1\fR
+SantaLucia 1998\&.
+\fIThis is the recommended value\fR\&.
+.RE
+.sp
+.RS 4
+.ie n \{\
+\h'-04'\(bu\h'+03'\c
+.\}
+.el \{\
+.sp -1
+.IP \(bu 2.3
+.\}
+\fI2\fR
+Owczarzy et al\&., 2004\&.
+.RE
+.RE
+.PP
+\fB\-i\fR
+.RS 4
+prints references to publications which were used for thermodynamic calculations\&.
+.RE
+.SH "REFERENCE"
+.PP
+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\&.
+.SH "SEE ALSO"
+.PP
+
+\fBprimer3_core\fR(1)
+\fBntdpal\fR(1)
+.SH "COPYRIGHT"
+.br
+Copyright \(co 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
+.br
+.PP
+All rights reserved\&. On Debian\-based systems, please consult
+/usr/share/doc/primer3/copyright
+to read the licence of oligotm\&.
+.PP
+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\&.
+
+.sp