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
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
|
<?xml version='1.0' encoding='UTF-8'?>
<!-- XML Authors: Corinne Maufrais, Nicolas Joly and Bertrand Neron, -->
<!-- 'Biological Software and Databases' Group, Institut Pasteur, Paris. -->
<!-- Distributed under LGPLv2 License. Please refer to the COPYING.LIB document. -->
<program>
<head>
<name>rnaeval</name>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/ViennaRNA_package.xml"/>
<doc>
<title>RNAeval</title>
<description>
<text lang="en">Calculate energy of RNA sequences on given secondary structure</text>
</description>
<authors>Hofacker, Stadler</authors>
<reference>I.L. Hofacker, W. Fontana, P.F. Stadler, S. Bonhoeffer, M. Tacker, P. Schuster (1994) Fast Folding and Comparison of RNA Secondary Structures. Monatshefte f. Chemie 125: 167-188</reference>
<doclink>http://www.tbi.univie.ac.at/RNA/RNAeval.html</doclink>
<comment>
<text lang="en">RNAeval evaluates the free energy of an RNA molecule in fixed secondary structure.</text>
</comment>
</doc>
<category>sequence:nucleic:2D_structure</category>
<category>structure:2D_structure</category>
</head>
<parameters>
<parameter iscommand="1" ishidden="1">
<name>rnaeval</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"RNAeval"</code>
<code proglang="python">"RNAeval"</code>
</format>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>seqstruct</name>
<prompt lang="en">Sequences/Structures File</prompt>
<type>
<datatype>
<class>RNAStructure</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">" < $value" </code>
<code proglang="python">" < " + str(value) </code>
</format>
<comment>
<text lang="en">Sequences and structures are read alternately from stdin.
The energy in Kcal/Mol is written to stdout.
The program will continue to read new sequences and structures until a line
consisting of the single character "@" or an end of file condition is encountered.
If the input sequence or structure contains the separator character "&" the program
calculates the energy of the co-folding of two RNA strands, where the "&" marks the
boundary between the two strands.</text>
</comment>
<example>
ACGAUCAGAGAUCAGAGCAUACGACAGCAG
..((((...))))...((........))..
UUUUUUUAAUAUAAA&AGACAAAAAGUCGGG
.(.(.(()).).)..&.(((.....)))...
@
</example>
<argpos>1000</argpos>
</parameter>
<paragraph>
<name>others_options</name>
<prompt lang="en">Other options</prompt>
<argpos>2</argpos>
<parameters>
<parameter>
<name>temperature</name>
<prompt lang="en">Rescale energy parameters to a temperature of temp C. (-T)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>37.0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -T $value" : ""</code>
<code proglang="python">( "" , " -T " + str(value) )[ value is not None and value != vdef]</code>
</format>
</parameter>
<parameter>
<name>tetraloops</name>
<prompt lang="en">Do not include special stabilizing energies for certain tetraloops (-4)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -4" : ""</code>
<code proglang="python">( "" , " -4" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>dangling</name>
<prompt lang="en">How to treat dangling end energies for bases adjacent to helices in free ends and multiloops (-d)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>-d1</value>
</vdef>
<vlist>
<velem>
<value>-d1</value>
<label>Only unpaired bases can participate in at most one dangling end (-d1)</label>
</velem>
<velem>
<value>-d</value>
<label>Ignores dangling ends altogether (-d)</label>
</velem>
<velem>
<value>-d2</value>
<label>The check is ignored, this is the default for partition function folding (-d2)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " $value" : ""</code>
<code proglang="python">( "" , " " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">How to treat 'dangling end' energies for bases adjacent to helices in free
ends and multiloops: Normally only unpaired bases can participate in at most one dangling end.
</text>
<text lang="en">
-d Do not give stabilizing energies to unpaired bases adjacent to helices in
multiloops and free ends ("dangling ends"). Same as -d0, opposite of -d1
(the default).
</text>
<text lang="en">
-d2 Treat dangling ends as in the partition function algorithm, i.e. bases adjacent
to helices in multiloops and free ends give a stabilizing energy contribution,
regardless whether they're paired or unpaired.
</text>
<text lang="en">
-d3 Allow coaxial stacking of adjacent helices in multi-loops.
</text>
</comment>
</parameter>
<parameter>
<name>logML</name>
<prompt lang="en">Let multiloop energies depend logarithmically on the size (-logML)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -logML" : ""</code>
<code proglang="python">( "" , " -logML" )[ value ]</code>
</format>
<comment>
<text lang="en">Let multiloop energies depend logarithmically on the size,
instead of the usual linear energy function.</text>
</comment>
</parameter>
<parameter>
<name>circular</name>
<prompt lang="en">-circ Assume a cricular (rather than linear) RNA molecule.</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -circ" : ""</code>
<code proglang="python">( "" , " -circ" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>parameter</name>
<prompt lang="en">Energy parameter file (-P)</prompt>
<type>
<datatype>
<class>EnergyParameterFile</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -P $value" : ""</code>
<code proglang="python">( "" , " -P " + str(value) )[ value is not None ]</code>
</format>
<comment>
<p xmlns="http://www.w3.org/1999/xhtml">Read energy parameters from paramfile, instead of using the default parameter set.
<a target="ParamFile" href="http://www.tbi.univie.ac.at/~ivo/RNA/RNAlib/Param-Files.html">( documentation for details on the file format.)</a>
</p>
</comment>
</parameter>
<!-- core dumped
<parameter>
<name>energy</name>
<prompt lang="en">Energy parameters for the artificial ABCD... alphabet (-e)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>Null</value>
</vdef>
<vlist>
<velem undef="1">
<value>Null</value>
<label>No energy for the artificial ABCD</label>
</velem>
<velem>
<value>1</value>
<label>Use energy parameters for GC pairs (1)</label>
</velem>
<velem>
<value>2</value>
<label>Use energy parameters for AU pairs (2)</label>
</velem>
</vlist>
<format>
<code proglang="perl">($value)? " -e $value" : ""</code>
<code proglang="python">( "" , " -e " + str(value) )[ value is not None ]</code>
</format>
</parameter>
-->
<paragraph>
<name>output_options</name>
<prompt lang="en">Output options</prompt>
<parameters>
<parameter>
<name>verbose</name>
<prompt lang="en"> Print out energy contribution of each loop in the structure.</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -v ": ""</code>
<code proglang="python">( "" , " -v ")[ value ]</code>
</format>
</parameter>
</parameters>
</paragraph>
</parameters>
</paragraph>
</parameters>
</program>
|
