/var/lib/mobyle/programs/rnaup.xml is in mobyle-programs 5.1.2-1.
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<!-- 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>rnaup</name>
<version>1.8.4</version>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/ViennaRNA_package.xml"/>
<doc>
<title>RNAup</title>
<description>
<text lang="en">Calculate the thermodynamics of RNA-RNA interactions</text>
</description>
<authors>Ivo L Hofacker, Peter F Stadler, Stephan Bernhart</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>
<reference>S.H.Bernhart, Ch. Flamm, P.F. Stadler, I.L. Hofacker Partition Function and Base Pairing Probabilities of RNA Heterodimers Algorithms Mol. Biol. (2006)</reference>
<reference>D.H. Mathews, J. Sabina, M. Zuker and H. Turner "Expanded Sequence Dependence of Thermodynamic Parameters Provides Robust Prediction of RNA Secondary Structure" JMB, 288, pp 911-940, 1999</reference>
<doclink>http://bioweb2.pasteur.fr/gensoft/sequence/nucleic/2D_structure.html#ViennaRNa</doclink>
<comment>
<text lang="en">RNAup calculates the thermodynamics of RNA-RNA interactions, by decomposing the
binding into two stages. </text>
<text lang="en">(1) First the probability that a
potential binding sites remains unpaired (equivalent to the free energy
needed to open the site) is computed. </text>
<text lang="en">(2) Then this accessibility is
combined with the interaction energy to obtain the total binding
energy. </text>
<text lang="en">All calculations are done by computing partition functions over
all possible conformations.</text>
</comment>
</doc>
<category>sequence:nucleic:2D_structure</category>
<command>RNAup</command>
</head>
<parameters>
<parameter ismandatory="1" issimple="1">
<name>seq</name>
<prompt lang="en">RNA Sequences File</prompt>
<type>
<biotype>RNA</biotype>
<datatype>
<class>RNASequence</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">" < $value" </code>
<code proglang="python">" < " + str(value) </code>
</format>
<argpos>1000</argpos>
<comment>
<text lang="en">Each line of file corresponds to one sequence, except for lines starting with ">" which contain the name of the next sequence. To compute the hybrid structure of two molecules, the two sequences must be concatenated using the & character as separator.</text>
</comment>
<example>
ACGAUCAGAGAUCAGAGCAUACGACAGCAG&ACGAAAAAAAGAGCAUACGACAGCAG
</example>
</parameter>
<paragraph>
<name>freeEnergie</name>
<prompt lang="en">Options for calculation of free energies</prompt>
<argpos>2</argpos>
<parameters>
<parameter>
<name>partition_free</name>
<prompt lang="en">Specifies the length of the unstructured region (-u)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>4</value>
</vdef>
<format>
<code proglang="perl">($value)? " -u $value" : ""</code>
<code proglang="python">( "" , " -u "+ str(value) )[ value is not None and value != vdef ]</code>
</format>
<comment>
<text lang="en">Specifies the length (len) of the unstructured region in the
output. The default value is 4. The probability of being
unpaired is plotted on the right border of the unpaired region.
You can specify up to 20 different length values: use "-" to
specify a range of continuous values (e.g. -u 4-8) or specify a
list of comma separated values (e.g. -u 4,8,15).</text>
</comment>
</parameter>
<parameter>
<name>shime</name>
<prompt lang="en">Option allows to get the different contributions to the probability of being unpaired. (-c)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">($value)? " -c $value" : ""</code>
<code proglang="python">( "" , " -c " +str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">by default only the full probability of being unpaired is plot-
ted. The -c option allows to get the different contributions (c)
to the probability of being unpaired: The full probability of
being unpaired ("S") is the sum of the probability of being
unpaired in the exterior loop ("E"), within a hairpin loop
("H"), within an interior loop ("I") and within a multiloop
("M"). Any combination of these letters may be given.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>interaction</name>
<prompt lang="en">Options for calculation of interaction</prompt>
<argpos>2</argpos>
<parameters>
<parameter>
<name>Length</name>
<prompt lang="en">Determines the maximal length of the region of interaction (-w)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>25</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -w $value" : ""</code>
<code proglang="python">( "" , " -w " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Determines the maximal length of the region of interaction, the
default is 25.</text>
</comment>
</parameter>
<parameter>
<name>unpaired</name>
<prompt lang="en">Include the probability of unpaired regions in both RNAs (-b)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -b " : ""</code>
<code proglang="python">( "" , " -b " )[ value ]</code>
</format>
<comment>
<text lang="en">Include the probability of unpaired regions in both (b) RNAs. By
default only the probability of being unpaired in the longer RNA
(target) is used.</text>
</comment>
</parameter>
<parameter>
<name>side5</name>
<prompt lang="en">Extend the region of interaction in the target by len residues to the 5' side</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -5 $value" : ""</code>
<code proglang="python">( "" , " -5 " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en"> These options extend the region of interaction in the target by
len residues to the 5' and 3' side, respectively. The underlying
assumption is that it is favorable for an interaction if not
only the direct region of contact is unpaired but also a few
residues 5' and 3' of this region.</text>
</comment>
</parameter>
<parameter>
<name>side3</name>
<prompt lang="en">Extend the region of interaction in the target by len residues to the 3' side</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -3 $value" : ""</code>
<code proglang="python">( "" , " -3 " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en"> These options extend the region of interaction in the target by
len residues to the 5' and 3' side, respectively. The underlying
assumption is that it is favorable for an interaction if not
only the direct region of contact is unpaired but also a few
residues 5' and 3' of this region.</text>
</comment>
</parameter>
<parameter>
<name>interaction</name>
<prompt lang="en">Interaction mode</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>null</value>
</vdef>
<vlist>
<velem undef="1">
<value>null</value>
<label></label>
</velem>
<velem>
<value>-Xp</value>
<label>Pairwise interaction is calculated (-Xp)</label>
</velem>
<velem>
<value>-Xf</value>
<label>The interaction of each sequence with the first one is calculated (-Xf)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " $value" : ""</code>
<code proglang="python">( "" , " " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Xp: Pairwise (p) interaction is calculated:
The first sequence interacts with the 2nd, the third with the
4th etc. If -Xp is selected two interacting sequences may be
given in a single line separated by "&" or each sequence may be
given on an extra line.</text>
<text lang="en">Xf: The interaction of each sequence with the
first one is calculated (e.g. interaction of one mRNA with many
small RNAs). Each sequence has to be given on an extra line.
</text>
</comment>
</parameter>
<parameter>
<name>target</name>
<prompt lang="en">Use the first sequence in the input file as the target</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef)? " -target " : ""</code>
<code proglang="python">( "" , " -target " )[ value ]</code>
</format>
<comment>
<text lang="en">Use the first sequence in the input file as the target. No
length check is done</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>general</name>
<prompt lang="en">General option</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>Integer</class>
</datatype>
</type>
<vdef>
<value>37</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. With -d2 this check is ignored, this is the default for partition function folding (-p). -d ignores dangling ends altogether. Note that by default pf and mfe folding treat dangling ends differently, use -d2 (or -d) in addition to -p to ensure that both algorithms use the same energy model. The -d2 options is available for RNAfold, RNAeval, and RNAinverse only.</text>
</comment>
</parameter>
<parameter>
<name>scale</name>
<prompt lang="en">Use scale*mfe as an estimate for the free energy (-S)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -S $value" : ""</code>
<code proglang="python">( "" , " -S " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">In the calculation of the pf use scale*mfe as an estimate for the ensemble free energy (used to avoid overflows). The default is 1.07, usefull values are 1.0 to 1.2. Occasionally needed for long sequences. You can also recompile the programm to use double precision (see the README file).</text>
</comment>
</parameter>
<!-- core dumped
<parameter>
<name>constraints</name>
<prompt lang="en">Calculate structures subject to constraints (-C)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -C" : ""</code>
<code proglang="python">( "" , " -C" )[ value ]</code>
</format>
<comment>
<text lang="en">The programm reads first the sequence then the a string containg constraints on the structure encoded with the symbols: </text>
<text lang="en">| (the corresponding base has to be paired x (the base is unpaired)</text>
<text lang="en">< (base i is paired with a base j>i)</text>
<text lang="en">> (base i is paired with a base j<i)</text>
<text lang="en">matching brackets ( ) (base i pairs base j)</text>
<text lang="en">Pf folding ignores constraints of type '|' '<' and '>', but disallow all pairs conflicting with a constraint of type 'x' or '( )'. This is usually sufficient to enforce the constraint.</text>
</comment>
</parameter>
-->
<parameter>
<name>noLP</name>
<prompt lang="en">Avoid lonely pairs (helices of length 1) (-noLP)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -noLP" : ""</code>
<code proglang="python">( "" , " -noLP" )[ value ]</code>
</format>
<comment>
<text lang="en">Produce structures without lonely pairs (helices of length 1). For partition function folding this only disallows pairs that can only occur isolated. Other pairs may still occasionally occur as helices of length 1.</text>
</comment>
</parameter>
<parameter>
<name>noGU</name>
<prompt lang="en">Do not allow GU pairs (-noGU)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -noGU" : ""</code>
<code proglang="python">( "" , " -noGU" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>noCloseGU</name>
<prompt lang="en">Do not allow GU pairs at the end of helices (-noCloseGU)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -noCloseGU" : ""</code>
<code proglang="python">( "" , " -noCloseGU" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>nsp</name>
<prompt lang="en">Non standard pairs (comma seperated list) (-nsp)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -nsp $value" : "" </code>
<code proglang="python">( "" , " -nsp " + str(value) )[ value is not None ]</code>
</format>
<comment>
<text lang="en">Allow other pairs in addition to the usual AU,GC,and GU pairs. pairs is a comma seperated list of additionally allowed pairs. If a the first character is a '-' then AB will imply that AB and BA are allowed pairs. e.g. RNAfold -nsp -GA will allow GA and AG pairs. Nonstandard pairs are given 0 stacking energy.</text>
</comment>
</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>
<text lang="en">Read energy parameters from paramfile, instead of using the default parameter set. A sample parameterfile should accompany your distribution. See the RNAlib documentation for details on the file format.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<parameter isout="1">
<name>outfiles</name>
<prompt lang="en">RNAup output</prompt>
<type>
<datatype>
<class>RNAupOut</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<filenames>
<code proglang="perl">"RNA*.out"</code>
<code proglang="python">"RNA*.out"</code>
</filenames>
</parameter>
</parameters>
</program>
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