1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
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
|
