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diff --git a/academic/primer3/man1/oligotm.1 b/academic/primer3/man1/oligotm.1 new file mode 100644 index 0000000000..ed9dcf7910 --- /dev/null +++ b/academic/primer3/man1/oligotm.1 @@ -0,0 +1,165 @@ +'\" 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 |