conf/settings/RNAalifoldParameters.xml

   1 <?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
   2 <runnerConfig>
   3         <runnerClassName>compbio.runner.structure.RNAalifold</runnerClassName>
   4         <options isRequired='false'>
   5                 <name>Endgaps</name>
   6                 <description>Score pairs with endgaps same as gap-gap pairs</description>
   7                 <optionNames>-E</optionNames>
   8         </options>
   9         <options isRequired='false'>
  10                 <name>Most Informative Sequence</name>
  11                 <description>Ouput Set of nucleotides with frequency > average</description>
  12                 <optionNames>--mis</optionNames>
  13         </options>
  14         <options isRequired='false'>
  15                 <name>Partition Function</name>
  16                 <description>Output partition function and probability matrix</description>
  17                 <optionNames>-p</optionNames>
  18         </options>
  19         <options isRequired='false'>
  20                 <name>Circular</name>
  21                 <description>Assume circular RNA molecule</description>
  22                 <optionNames>-c</optionNames>
  23         </options>
  24         <!--  Not Currently available with circular structures (-c) -->
  25         <options isRequired='false'>
  26                 <name>G-Quadruplex</name>
  27                 <description>Incorporate G-Quadruplex formation into prediction algorithm</description>
  28                 <optionNames>-g</optionNames>
  29         </options>
  30         <options isRequired='false'>
  31                 <name>d2</name>
  32                 <description>dangling energies will be added for the bases adjacent to a helix on both sides</description>
  33                 <optionNames>-d2</optionNames>
  34         </options>
  35         <options isRequired='false'>
  36                 <name>No LP</name>
  37                 <description>Produce Structures without lonely pairs</description>
  38                 <optionNames>--noLP</optionNames>
  39         </options>
  40         <options isRequired='false'>
  41                 <name>No GU</name>
  42                 <description>Do not allow GU pairs</description>
  43                 <optionNames>--noGU</optionNames>
  44         </options>
  45         <options isRequired='false'>
  46                 <name>No Closing GU</name>
  47                 <description>Do not allow GU pairs at the end of sequences</description>
  48                 <optionNames>--noClosingGU</optionNames>
  49         </options>
  50         <options isRequired='false'>
  51                 <name>old</name>
  52                 <description>Use old energy evaluation, treating gaps as characters</description>
  53                 <optionNames>--old</optionNames>
  54         </options>
  55         <options isRequired='false'>
  56                 <name>Ribosum Scoring</name>
  57                 <description>Use Ribosum Scoring Matrix</description>
  58                 <optionNames>-r</optionNames>
  59         </options>
  60         <options isRequired='false'>
  61                 <name>d2</name>
  62                 <description>
  63                 Dangling energies are added for the bases adjacent to a helix on both sides
  64                 </description>
  65                 <optionNames>-d2</optionNames>
  66         </options>
  67         <options isRequired='false'>
  68                 <name>MEA Structure</name>
  69                 <description>Maximum Expected Accuracy Structure</description>
  70                 <optionNames>--MEA</optionNames>
  71         </options>
  72
  73         <prmSeparator> </prmSeparator>
  74
  75         <parameters isRequired='false'>
  76                 <name>scaling factor</name>
  77                 <description>In calculating pf use scale*mfe as estimate for ensemble free energy]</description>
  78                 <optionNames>-S</optionNames>
  79                 <defaultValue>1.07</defaultValue>
  80                 <validValue>
  81                         <type>Float</type>
  82                         <min>0</min>
  83                         <max>100</max>
  84                 </validValue>
  85         </parameters>
  86         <parameters isRequired='false'>
  87                 <name>bppmThreshold</name>
  88                 <description>Threshold for base pair probabilities</description>
  89                 <optionNames>--bppmThreshold</optionNames>
  90                 <defaultValue>0.000001</defaultValue>
  91                 <validValue>
  92                         <type>Float</type>
  93                         <min>0.0000000000001</min>
  94                         <max>1.0</max>
  95                 </validValue>
  96         </parameters>
  97         <parameters isRequired='false'>
  98                 <name>Temperature</name>
  99                 <description>Rescale Energy parameters to Temperature</description>
 100                 <optionNames>-T</optionNames>
 101                 <defaultValue>37</defaultValue>
 102                 <validValue>
 103                         <type>Float</type>
 104                         <min>-274</min>
 105                         <max>1000000</max>
 106                 </validValue>
 107         </parameters>
 108         <parameters isRequired='false'>
 109                 <name>cfactor</name>
 110                 <description>weight of covariance term</description>
 111                 <optionNames>--cfactor</optionNames>
 112                 <defaultValue>1.0</defaultValue>
 113                 <validValue>
 114                         <type>Float</type>
 115                         <min>0</min>
 116                         <max>100000</max>
 117                 </validValue>
 118         </parameters>
 119         <parameters isRequired='false'>
 120                 <name>nfactor</name>
 121                 <description>penalty for non-compatible sequences in covariance term</description>
 122                 <optionNames>--nfactor</optionNames>
 123                 <defaultValue>1.0</defaultValue>
 124                 <validValue>
 125                         <type>Float</type>
 126                         <min>0</min>
 127                         <max>100000</max>
 128                 </validValue>
 129         </parameters>
 130
 131 </runnerConfig>