/var/lib/mobyle/programs/rnadistance.xml is in mobyle-programs 5.1.1-1.
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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>rnadistance</name>
<xi:include xmlns:xi="http://www.w3.org/2001/XInclude" href="Entities/ViennaRNA_package.xml"/>
<doc>
<title>RNAdistance</title>
<description>
<text lang="en">Calculate distances between RNA secondary structures</text>
</description>
<authors>Hofacker, Fontana, Hofacker, Stadler</authors>
<reference>Shapiro B A, (1988) An algorithm for comparing multiple RNA secondary structures, CABIOS 4, 381-393 Shapiro B A, Zhang K (1990) Comparing multiple RNA secondary structures using tree comparison, CABIOS 6, 309-318</reference>
<reference>Fontana W, Konings D A M, Stadler P F, Schuster P, (1993) Statistics of RNA secondary structures, Biopolymers 33, 1389-1404 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>
<comment>
<text lang="en">RNAdistance reads RNA secondary structures from stdin and calculates one or more measures for their dissimilarity, based on tree or string editing (alignment). In addition it calculates a "base pair distance" given by the number of base pairs present in one structure, but not the other. For structures of different length base pair distance is not recommended.</text>
</comment>
</doc>
<category>sequence:nucleic:2D_structure</category>
<category>structure:2D_structure</category>
</head>
<parameters>
<parameter iscommand="1" ishidden="1">
<name>rnadistance</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"RNAdistance "</code>
<code proglang="python">"RNAdistance "</code>
</format>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>struct</name>
<prompt lang="en">RNA structures File</prompt>
<type>
<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">The program accepts structures in bracket format, where matching brackets symbolize base pairs and unpaired bases are represented by a dot '.', or coarse grained representations where hairpins, interior loops, bulges, multiloops, stacks and external bases are represented by (H), (I), (B), (M), (S), and (E), respectively. These can be optionally weighted. Full structures can be represented in the same fashion using the identifiers (U) and (P) for unpaired and paired bases, respectively. Examples:</text>
<text lang="en">.((..(((...)))..((..)))). full structure (usual format);</text>
<text lang="en">(U)((U2)((U3)P3)(U2)((U2)P2)P2) HIT structure;</text>
<text lang="en">((H)(H)M) or ((((H)S)((H)S)M)S) coarse grained structure;</text>
<text lang="en">(((((H3)S3)((H2)S2)M4)S2)E2) weighted coarse grained.</text>
</comment>
</parameter>
<paragraph>
<name>others_options</name>
<prompt lang="en">Other options</prompt>
<argpos>2</argpos>
<parameters>
<parameter>
<name>distance</name>
<prompt lang="en">Representation for distance calculation (-D)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>f</value>
</vdef>
<vlist>
<velem>
<value>f</value>
<label>Full tree editing (f)</label>
</velem>
<velem>
<value>F</value>
<label>Full string alignment (F)</label>
</velem>
<velem>
<value>h</value>
<label>HIT tree editing (h)</label>
</velem>
<velem>
<value>H</value>
<label>HIT string alignment (H)</label>
</velem>
<velem>
<value>w</value>
<label>Weighted coarse tree editing (w)</label>
</velem>
<velem>
<value>W</value>
<label>Weighted coarse string alignment (W)</label>
</velem>
<velem>
<value>c</value>
<label>Coarse tree editing (c)</label>
</velem>
<velem>
<value>C</value>
<label>Coarse string alignment (C)</label>
</velem>
<velem>
<value>P</value>
<label>Selects the base pair distance (P)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " -D$value" : ""</code>
<code proglang="python">( "" , " -D" +str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">Use the full, HIT, weighted coarse, or coarse representation to calculate the distance. Capital letters indicate string alignment otherwise tree editing is used. Any combination of distances can be specified. -DP selects the base pair distance. The default if "f".</text>
</comment>
</parameter>
<parameter>
<name>compare</name>
<prompt lang="en">Which comparisons (-X)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>p</value>
</vdef>
<vlist>
<velem>
<value>p</value>
<label>Pairwise (1st/2nd, 3rd/4th etc) (p)</label>
</velem>
<velem>
<value>m</value>
<label>Distance matrix between all structures (m)</label>
</velem>
<velem>
<value>f</value>
<label>Each structure to the first one (f)</label>
</velem>
<velem>
<value>c</value>
<label>Continuously, that is i-th with (i+1)th structure (c)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " -X$value" : ""</code>
<code proglang="python">( "" , " -X" +str(value) )[ value is not None and value != vdef]</code>
</format>
<comment>
<text lang="en">p: compare the structures pairwise (p), that is first with 2nd, third with 4th etc. This is the default.</text>
<text lang="en">m: calculate the distance matrix between all structures. The output is formatted as a lower triangle matrix.</text>
<text lang="en">f: compare each structure to the first one.</text>
<text lang="en">c: compare continuously, that is i-th with (i+1)th structure.</text>
</comment>
</parameter>
<paragraph>
<name>matrix_options</name>
<prompt lang="en">Analyse the distance matrix</prompt>
<precond>
<code proglang="perl">$compare eq "m"</code>
<code proglang="python">compare == "m"</code>
</precond>
<argpos>2000</argpos>
<comment>
<text lang="en">Only when comparison between all structures is requested (-Xm). This uses AnalyseDists distributed with the Vienna package.</text>
</comment>
<parameters>
<parameter>
<name>do_analyse</name>
<prompt lang="en">Do this analysis (AnalyseDists program)?</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " | AnalyseDists" : ""</code>
<code proglang="python">("", " | AnalyseDists")[value]</code>
</format>
<comment>
<text lang="en">AnalyseDists reads a distance matrix (given as lower triangle matrix) from stdin and writes a split decomposition and a cluster analysis of this distance matrix to stdout. </text>
</comment>
</parameter>
<parameter>
<name>Method</name>
<prompt lang="en">AnalyseDist methods to be used (-X)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>Null</value>
</vdef>
<vlist>
<velem undef="1">
<value>Null</value>
<label>Choose an analysis methods</label>
</velem>
<velem>
<value>s</value>
<label>Split decomposition (s)</label>
</velem>
<velem>
<value>w</value>
<label>Cluster analysis using Ward's method (w)</label>
</velem>
<velem>
<value>n</value>
<label>Cluster analysis using Saitou's neighbour joining method (n)</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef)? " -X$value" : "" </code>
<code proglang="python">("", " -X"+str(value))[ value is not None and value != vdef]</code>
</format>
<argpos>2001</argpos>
</parameter>
<parameter isout="1">
<name>psfiles</name>
<prompt lang="en">Postcript output file</prompt>
<type>
<datatype>
<class>PostScript</class>
<superclass>Binary</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$compare eq "m" and $Method ne "s"</code>
<code proglang="python">compare == "m" and Method != "s"</code>
</precond>
<filenames>
<code proglang="perl">"*.ps"</code>
<code proglang="python">"*.ps"</code>
</filenames>
</parameter>
</parameters>
</paragraph>
<parameter>
<name>shapiro</name>
<prompt lang="en">Use the Bruce Shapiro's cost matrix for comparing coarse structures (-S)</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value)? " -S" : ""</code>
<code proglang="python">( "" , " -S" )[ value ]</code>
</format>
</parameter>
<parameter>
<name>alignment_name</name>
<prompt lang="en">Structure alignment file (-B)</prompt>
<type>
<datatype>
<class>Filename</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value)? " -B $value" : ""</code>
<code proglang="python">( "" , " -B " +str(value) )[ value is not None]</code>
</format>
<comment>
<text lang="en">Print an 'alignment' with gaps of the structures, to show matching substructures. The aligned structures are written to file, if specified. Otherwise output is written to stdout, unless the -Xm option is set in which case 'backtrack.file' is used.</text>
</comment>
</parameter>
<parameter isout="1">
<name>ali_outfile</name>
<prompt lang="en">Alignment output file</prompt>
<type>
<datatype>
<class>RnadistanceReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$alignment_name</code>
<code proglang="python">alignment_name is not None</code>
</precond>
<filenames>
<code proglang="perl">$alignment_name</code>
<code proglang="python">str(alignment_name)</code>
</filenames>
</parameter>
</parameters>
</paragraph>
</parameters>
</program>
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