1 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
3 <runnerConfig xmlns:xsi="http://www.w3.org/2001/XMLSchema.dtd"
4 xsi:noNamespaceSchemaLocation="RunnerConfigSchema.xsd">
5 <runnerClassName>compbio.runner.structure.RNAalifold</runnerClassName>
6 <options isRequired='false'>
8 <description>Score pairs with endgaps same as gap-gap pairs</description>
9 <optionNames>-E</optionNames>
11 <options isRequired='false'>
12 <name>Most Informative Sequence</name>
13 <description>Ouput Set of nucleotides with frequency > average</description>
14 <optionNames>--mis</optionNames>
16 <options isRequired='false'>
17 <name>Partition Function</name>
18 <description>Output partition function and probability matrix</description>
19 <optionNames>-p</optionNames>
21 <options isRequired='false'>
23 <description>Assume circular RNA molecule</description>
24 <optionNames>-c</optionNames>
26 <!-- Not Currently available with circular structures (-c) -->
27 <options isRequired='false'>
28 <name>G-Quadruplex</name>
29 <description>Incorporate G-Quadruplex formation into prediction algorithm</description>
30 <optionNames>-g</optionNames>
32 <options isRequired='false'>
34 <description>dangling energies will be added for the bases adjacent to a helix on both sides</description>
35 <optionNames>-d2</optionNames>
37 <options isRequired='false'>
39 <description>Produce Structures without lonely pairs</description>
40 <optionNames>--noLP</optionNames>
42 <options isRequired='false'>
44 <description>Do not allow GU pairs</description>
45 <optionNames>--noGU</optionNames>
47 <options isRequired='false'>
48 <name>No Closing GU</name>
49 <description>Do not allow GU pairs at the end of sequences</description>
50 <optionNames>--noClosingGU</optionNames>
52 <options isRequired='false'>
54 <description>Use old energy evaluation, treating gaps as characters</description>
55 <optionNames>--old</optionNames>
57 <options isRequired='false'>
58 <name>Ribosum Scoring</name>
59 <description>Use Ribosum Scoring Matrix</description>
60 <optionNames>-r</optionNames>
62 <options isRequired='false'>
65 Dangling energies are added for the bases adjacent to a helix on both sides
67 <optionNames>-d2</optionNames>
69 <options isRequired='false'>
70 <name>MEA Structure</name>
71 <description>Maximum Expected Accuracy Structure</description>
72 <optionNames>--MEA</optionNames>
75 <prmSeparator> </prmSeparator>
77 <parameters isRequired='false'>
78 <name>scaling factor</name>
79 <description>In calculating pf use scale*mfe as estimate for ensemble free energy]</description>
80 <optionNames>-S</optionNames>
81 <defaultValue>1.07</defaultValue>
88 <parameters isRequired='false'>
89 <name>bppmThreshold</name>
90 <description>Threshold for base pair probabilities</description>
91 <optionNames>--bppmThreshold</optionNames>
92 <defaultValue>0.000001</defaultValue>
95 <min>0.0000000000001</min>
99 <parameters isRequired='false'>
100 <name>Temperature</name>
101 <description>Rescale Energy parameterss to Temperature</description>
102 <optionNames>-T</optionNames>
103 <defaultValue>37</defaultValue>
111 <parameters isRequired='false'>
113 <description>weight of covariance term</description>
114 <optionNames>--cfactor</optionNames>
115 <defaultValue>1.0</defaultValue>
122 <parameters isRequired='false'>
124 <description>penalty for non-compatible sequences in covariance term</description>
125 <optionNames>--nfactor</optionNames>
126 <defaultValue>1.0</defaultValue>