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
166
|
'\" t
.\" Title: PRIMA
.\" Author: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
.\" Date: 05/11/2012
.\" Manual: EMBOSS Manual for Debian
.\" Source: EMBOSS 6.4.0
.\" Language: English
.\"
.TH "PRIMA" "1e" "05/11/2012" "EMBOSS 6.4.0" "EMBOSS Manual for Debian"
.\" -----------------------------------------------------------------
.\" * 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"
prima \- Selects primers for PCR and DNA amplification\&.
.SH "SYNOPSIS"
.HP \w'\fBprima\fR\ 'u
\fBprima\fR \fB\-sequence\ \fR\fB\fIsequence\fR\fR \fB\-targetrange\ \fR\fB\fItoggle\fR\fR \fB\-targetstart\ \fR\fB\fIinteger\fR\fR \fB\-targetend\ \fR\fB\fIinteger\fR\fR \fB\-mintmprimer\ \fR\fB\fIfloat\fR\fR \fB\-maxtmprimer\ \fR\fB\fIfloat\fR\fR \fB\-minplen\ \fR\fB\fIinteger\fR\fR \fB\-maxplen\ \fR\fB\fIinteger\fR\fR \fB\-minpgccont\ \fR\fB\fIfloat\fR\fR \fB\-maxpgccont\ \fR\fB\fIfloat\fR\fR [\fB\-primer\ \fR\fB\fItoggle\fR\fR] \fB\-minprimerlen\ \fR\fB\fIinteger\fR\fR \fB\-maxprimerlen\ \fR\fB\fIinteger\fR\fR \fB\-minpmgccont\ \fR\fB\fIfloat\fR\fR \fB\-maxpmgccont\ \fR\fB\fIfloat\fR\fR \fB\-overlap\ \fR\fB\fIinteger\fR\fR \fB\-saltconc\ \fR\fB\fIfloat\fR\fR \fB\-dnaconc\ \fR\fB\fIfloat\fR\fR \fB\-list\ \fR\fB\fIboolean\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
.HP \w'\fBprima\fR\ 'u
\fBprima\fR \fB\-help\fR
.SH "DESCRIPTION"
.PP
\fBprima\fR
is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Nucleic:Primers" command group(s)\&.
.SH "OPTIONS"
.SS "Input section"
.PP
\fB\-sequence\fR \fIsequence\fR
.RS 4
.RE
.SS "Required section"
.SS "Target options"
.PP
\fB\-targetrange\fR \fItoggle\fR
.RS 4
Default value: N
.RE
.PP
\fB\-targetstart\fR \fIinteger\fR
.RS 4
Default value: $(sequence\&.begin)
.RE
.PP
\fB\-targetend\fR \fIinteger\fR
.RS 4
Default value: $(sequence\&.length)
.RE
.PP
\fB\-mintmprimer\fR \fIfloat\fR
.RS 4
Default value: 53
.RE
.PP
\fB\-maxtmprimer\fR \fIfloat\fR
.RS 4
Default value: 58
.RE
.SS "Additional section"
.SS "Product options"
.PP
\fB\-minplen\fR \fIinteger\fR
.RS 4
Default value: 100
.RE
.PP
\fB\-maxplen\fR \fIinteger\fR
.RS 4
Default value: 300
.RE
.PP
\fB\-minpgccont\fR \fIfloat\fR
.RS 4
Default value: \&.40
.RE
.PP
\fB\-maxpgccont\fR \fIfloat\fR
.RS 4
Default value: \&.55
.RE
.SS "Primer options"
.PP
\fB\-primer\fR \fItoggle\fR
.RS 4
Specify primer properties Default value: Y
.RE
.PP
\fB\-minprimerlen\fR \fIinteger\fR
.RS 4
Default value: 18
.RE
.PP
\fB\-maxprimerlen\fR \fIinteger\fR
.RS 4
Default value: 22
.RE
.PP
\fB\-minpmgccont\fR \fIfloat\fR
.RS 4
Default value: \&.40
.RE
.PP
\fB\-maxpmgccont\fR \fIfloat\fR
.RS 4
Default value: \&.55
.RE
.SS "Advanced section"
.PP
\fB\-overlap\fR \fIinteger\fR
.RS 4
Default value: 50
.RE
.PP
\fB\-saltconc\fR \fIfloat\fR
.RS 4
Default value: 50
.RE
.PP
\fB\-dnaconc\fR \fIfloat\fR
.RS 4
Default value: 50
.RE
.PP
\fB\-list\fR \fIboolean\fR
.RS 4
Default value: N
.RE
.SS "Output section"
.PP
\fB\-outfile\fR \fIoutfile\fR
.RS 4
.RE
.SH "BUGS"
.PP
Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
.SH "SEE ALSO"
.PP
prima is fully documented via the
\fBtfm\fR(1)
system\&.
.SH "AUTHOR"
.PP
\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging@lists\&.alioth\&.debian\&.org\&>
.RS 4
Wrote the script used to autogenerate this manual page\&.
.RE
.SH "COPYRIGHT"
.br
.PP
This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
.sp
|
