/var/lib/mobyle/programs/rnainverse.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 xmlns:xi="http://www.w3.org/2001/XInclude" >
<head>
<name>rnainverse</name>
<xi:include href="Entities/ViennaRNA_package.xml"/>
<doc>
<title>RNAinverse</title>
<description>
<text lang="en">Find RNA sequences with given secondary structure</text>
</description>
<authors>Hofacker</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>A. Walter, D Turner, J Kim, M Lyttle, P Muller, D Mathews, M Zuker Coaxial stacking of helices enhances binding of oligoribonucleotides. PNAS, 91, pp 9218-9222, 1994</reference>
<reference>M. Zuker, P. Stiegler (1981) Optimal computer folding of large RNA sequences using thermodynamic and auxiliary information, Nucl Acid Res 9: 133-148</reference>
<reference>J.S. McCaskill (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structures, Biopolymers 29: 11051119 D.H. Turner N. Sugimoto and S.M. Freier (1988) RNA structure prediction, Ann Rev Biophys Biophys Chem 17: 167-192</reference>
<reference>D. Adams (1979) The hitchhiker's guide to the galaxy, Pan Books, London</reference>
<comment>
<text lang="en">RNAinverse searches for sequences folding into a predefined structure, thereby inverting the folding algorithm. Target structures (in bracket notation) and starting sequences for the search are read alternately from file.
</text>
</comment>
</doc>
<category>sequence:nucleic:2D_structure</category>
<category>structure:2D_structure</category>
</head>
<parameters>
<parameter iscommand="1" ishidden="1">
<name>rnainverse</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>rnainverse</value>
</vdef>
<format>
<code proglang="perl">"RNAinverse"</code>
<code proglang="python">"RNAinverse"</code>
</format>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>seq</name>
<prompt lang="en">Structures File</prompt>
<type>
<biotype>RNA</biotype>
<datatype>
<class>RNAStructure</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">Target structures and starting sequences for the search. </text>
</comment>
<example>
(((.(((....))).)))
NNNgNNNNNNNNNNaNNN
</example>
</parameter>
<paragraph>
<name>control</name>
<prompt lang="en">Control options</prompt>
<argpos>2</argpos>
<parameters>
<parameter>
<name>folding</name>
<prompt lang="en">Folding method (-F)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>m</value>
</vdef>
<vlist>
<velem>
<value>m</value>
<label>Minimum energy (m)</label>
</velem>
<velem>
<value>p</value>
<label>Partition function (p)</label>
</velem>
<velem>
<value>mp</value>
<label>Both (mp)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " -F$value" : ""</code>
<code proglang="python">("", " -F" + str(value))[ value is not None]</code>
</format>
<comment>
<text lang="en">Use minimum energy (-Fm), partition function folding (-Fp) or both (-Fmp). In partition function mode, the probability of the target structure exp(-E(S)/kT)/Q is maximized. This probability is written in brackets after the found sequence and Hamming distance. In most cases you'll want to use the -f option in conjunction with -Fp, see below. The default is -Fm.</text>
</comment>
</parameter>
<parameter>
<name>final</name>
<prompt lang="en">Stop search when sequence is found with E(s)-F smaller than this value (-f)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<precond>
<code proglang="perl">$folding eq 'mp' or $folding eq 'p'</code>
<code proglang="python">folding == 'mp' or folding == 'p'</code>
</precond>
<format>
<code proglang="perl">(defined $value)? " -f $value" : ""</code>
<code proglang="python">("", " -f " + str(value))[ value is not None]</code>
</format>
<comment>
<text lang="en">In combination with -Fp</text>
<text lang="en">F=-kT*ln(Q)</text>
</comment>
</parameter>
<parameter>
<name>repeats</name>
<prompt lang="en">Search repeatedly for the same structure (-R)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -R $value" : ""</code>
<code proglang="python">("", " -R " + str(value))[ value is not None]</code>
</format>
<comment>
<text lang="en">Search repeatedly for the same structure. If repeats is negative search until -repeats exact solutions are found, no output is done for unsuccessful searches. Be aware, that the program will not terminate if the target structure can not be found.</text>
</comment>
</parameter>
<parameter>
<name>alphabet</name>
<prompt lang="en">Find sequences using only bases from this alphabet (-a)</prompt>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -a $value" : ""</code>
<code proglang="python">("", " -a " + str(value))[ value is not None]</code>
</format>
</parameter>
</parameters>
</paragraph>
<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 temperature Celcius (-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)? " $value" : ""</code>
<code proglang="python">( "" , " " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">How to treat 'dangling end' energies for bases adjacent to helices in free ends and multiloops: Normally only unpaired bases can participate in at most one dangling end. With -d2 this check is ignored, this is the default for partition function folding (-p). -d ignores dangling ends altogether. Note that by default pf and mfe folding treat dangling ends differently, use -d2 (or -d) in addition to -p to ensure that both algorithms use the same energy model. The -d2 options is available for RNAfold, RNAeval, and RNAinverse only.</text>
</comment>
</parameter>
<parameter>
<name>noGU</name>
<prompt lang="en">Do not allow GU pairs (-noGU)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($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">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>
<!-- core dumped on raclette
<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">(defined $value and $value != $vdef)? " -e $value" : ""</code>
<code proglang="python">( "" , " -e " + str(value) )[ value is not None and value!=vdef]</code>
</format>
</parameter>
-->
</parameters>
</paragraph>
<!--
<parameter ishidden="1">
<name>readseq</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"<xi:include href="../../Local/Services/Programs/Env/ViennaRNA_readseq.xml" xpointer="xpointer(/readseq_path/text())"><xi:fallback/></xi:include>readseq -f=19 -a $seq > $seq.tmp && (cp $seq $seq.orig && mv $seq.tmp $seq) ; "</code>
<code proglang="python">"<xi:include href="../../Local/Services/Programs/Env/ViennaRNA_readseq.xml" xpointer="xpointer(/readseq_path/text())"><xi:fallback/></xi:include>readseq -f=19 -a "+ str(seq) + " > "+ str(seq) +".tmp && (cp "+ str(seq) +" "+ str(seq) +".orig && mv "+ str(seq) +".tmp "+ str(seq) +") ; "</code>
</format>
<argpos>-10</argpos>
</parameter>
-->
</parameters>
</program>
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