/var/lib/mobyle/programs/rnasubopt.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>rnasubopt</name>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/ViennaRNA_package.xml"/>
<doc>
<title>RNAsubopt</title>
<description>
<text lang="en">Calculate suboptimal secondary structures of RNAs</text>
</description>
<authors>Wuchty, Hofacker, Fontana</authors>
<reference>S. Wuchty, W. Fontana, I. L. Hofacker and P. Schuster Complete Suboptimal Folding of RNA and the Stability of Secondary Structures, Biopolymers, 49, 145-165 (1999)</reference>
<comment>
<text lang="en">RNAsubopt reads RNA sequences from file and (in the default -e mode) calculates all suboptimal secondary structures within a user defined energy range above the minimum free energy (mfe).It prints the suboptimal structures in bracket notation followed by the energy in kcal/mol to stdout. Be careful, the number of structures returned grows exponentially with both sequence length and energy range.</text>
<text lang="en">Alternatively, when used with the -p option, RNAsubopt produces Boltzmann weighted samples of secondary structures.</text>
</comment>
</doc>
<category>sequence:nucleic:2D_structure</category>
<category>structure:2D_structure</category>
</head>
<parameters>
<parameter iscommand="1" ishidden="1">
<name>rnasubopt</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<vdef>
<value>rnasubopt</value>
</vdef>
<format>
<code proglang="perl">"RNAsubopt"</code>
<code proglang="python">"RNAsubopt"</code>
</format>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>seq</name>
<prompt lang="en">RNA Sequences File</prompt>
<type>
<biotype>RNA</biotype>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>FASTA</dataFormat>
</type>
<format>
<code proglang="perl">" < $value" </code>
<code proglang="python">" < " + str(value)</code>
</format>
<argpos>1000</argpos>
</parameter>
<paragraph>
<name>control</name>
<prompt lang="en">Control options</prompt>
<argpos>2</argpos>
<parameters>
<parameter>
<name>mfe</name>
<prompt lang="en">Calculate suboptimal structures within this range kcal/mol of the mfe (-e)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<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>
<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>-d2</value>
</vdef>
<vlist>
<velem>
<value>-d1</value>
<label>Only unpaired bases can participate in at most one dangling end (-d1)</label>
</velem>
<velem>
<value>-d0</value>
<label>Ignores dangling ends altogether (-d0)</label>
</velem>
<velem>
<value>-d2</value>
<label>The check is ignored (-d2)</label>
</velem>
<velem>
<value>-d3</value>
<label>Coaxial stacking of adjacent helices in multi-loops (-d3)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " $value" : ""</code>
<code proglang="python">( "" , " " + str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Change treatment of dangling ends, as in RNAfold and RNAeval. The default is -d2 (as in partition function folding). If -d1 or -d3 are specified the structures are generated as with -d2 but energies are re-evaluated before printing.</text>
</comment>
</parameter>
<parameter>
<name>logML</name>
<prompt lang="en">Recalculate energies of structures using a logarithmic energy function for multi-loops (-logML)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -logML" : ""</code>
<code proglang="python">("", " -logML")[ value ]</code>
</format>
<comment>
<text lang="en">This option does not effect structure generation, only the energies that is printed out. Since logML lowers energies somewhat, some structures may be missing.</text>
</comment>
</parameter>
<parameter>
<name>ep</name>
<prompt lang="en">Only print structures with energy within this prange of the mfe (-ep)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -ep $value" : ""</code>
<code proglang="python">("", " -ep " + str(value))[ value is not None]</code>
</format>
<comment>
<text lang="en">Only print structures with energy within prange of the mfe. Useful in conjunction with -logML, -d1 or -d3: while the -e option specifies the range before energies are re-evaluated, -ep specifies the maximum energy after re-evaluation.</text>
</comment>
</parameter>
<parameter>
<name>sort</name>
<prompt lang="en">Sort the structures by energy (-s)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -s" : ""</code>
<code proglang="python">("", " -s")[value]</code>
</format>
<comment>
<text lang="en"> Since the sort in is done in memory, this
becomes impractical when the number of structures produced goes into millions.</text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>input</name>
<prompt lang="en">Input parameters</prompt>
<argpos>2</argpos>
<parameters>
<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">($value)? " -noLP" : ""</code>
<code proglang="python">("", " -noLP")[value]</code>
</format>
<comment>
<text lang="en">Only produce structures without lonely pairs (helices of length 1). This reduces the number of structures drastically and should therefore be used for longer sequences and larger energy ranges.</text>
</comment>
</parameter>
<parameter>
<name>noGU</name>
<prompt lang="en">Do not allow GU pairs (-noGU)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($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>
<parameter>
<name>z</name>
<prompt lang="en">Calculate z score</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">(defined $value)? " -z" : ""</code>
<code proglang="python">( "" , " -z" )[ value ]</code>
</format>
</parameter>
</parameters>
</paragraph>
<parameter ishidden="1">
<name>readseq</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" 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 xmlns:xi="http://www.w3.org/2001/XInclude" 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>
<parameter isout="1">
<name>psfiles</name>
<prompt>Postscript file</prompt>
<type>
<datatype>
<class>PostScript</class>
<superclass>Binary</superclass>
</datatype>
</type>
<filenames>
<code proglang="perl">"*.ps"</code>
<code proglang="python">"*.ps"</code>
</filenames>
</parameter>
</parameters>
</program>
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