/var/lib/mobyle/programs/mfold.xml is in mobyle-programs 5.1.2-2.
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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>mfold</name>
<version>3.6</version>
<doc>
<title>MFOLD</title>
<description>
<text lang="en">Prediction of RNA secondary structure</text>
</description>
<authors>M. Zuker</authors>
<reference>M. Zuker, D.H. Mathews and D.H. Turner Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide in RNA Biochemistry and Biotechnology, J. Barciszewski and B.F.C. Clark, eds., NATO ASI Series, Kluwer Academic Publishers, (1999)</reference>
<doclink>http://bioweb2.pasteur.fr/docs/mfold/index.html</doclink>
<homepagelink>http://www.bioinfo.rpi.edu/applications/mfold/</homepagelink>
<sourcelink>http://www.bioinfo.rpi.edu/~zukerm/export/</sourcelink>
</doc>
<category>sequence:nucleic:2D_structure</category>
<category>structure:2D_structure</category>
</head>
<parameters>
<parameter iscommand="1" ishidden="1">
<name>mfold</name>
<type>
<datatype>
<class>String</class>
</datatype>
</type>
<format>
<code proglang="perl">"mfold"</code>
<code proglang="python">"mfold"</code>
</format>
<argpos>0</argpos>
</parameter>
<parameter ismandatory="1" issimple="1">
<name>SEQ</name>
<prompt lang="en">Sequence File (SEQ)</prompt>
<type>
<biotype>DNA</biotype>
<datatype>
<class>Sequence</class>
</datatype>
<dataFormat>IG</dataFormat>
<dataFormat>GENBANK</dataFormat>
<dataFormat>EMBL</dataFormat>
</type>
<format>
<code proglang="perl">" SEQ=$value"</code>
<code proglang="python">" SEQ=" + str(value)</code>
</format>
<argpos>1</argpos>
<comment>
<text lang="en">SEQ : The sequence file may contain multiple sequences.
At present, the mfold script will fold the first sequence by default.</text>
</comment>
</parameter>
<parameter issimple="1">
<name>NA</name>
<prompt lang="en">RNA or DNA (NA)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>RNA</value>
</vdef>
<vlist>
<velem>
<value>RNA</value>
<label>RNA</label>
</velem>
<velem>
<value>DNA</value>
<label>DNA</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " NA=$value" : ""</code>
<code proglang="python">("" , " NA=" + str(value))[ value is not None and value != vdef]</code>
</format>
<argpos>2</argpos>
</parameter>
<parameter issimple="1">
<name>LC</name>
<prompt lang="en">Sequence type (LC)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>linear</value>
</vdef>
<vlist>
<velem>
<value>linear</value>
<label>Linear</label>
</velem>
<velem>
<value>circular</value>
<label>Circular</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " LC=$value" : ""</code>
<code proglang="python">("" , " LC=" + str(value))[ value is not None and value != vdef]</code>
</format>
<argpos>2</argpos>
<comment>
<text lang="en">It indicates whether a linear or circular nucleic acid is being folded.</text>
</comment>
</parameter>
<paragraph>
<name>control</name>
<prompt lang="en">Control options</prompt>
<argpos>3</argpos>
<parameters>
<parameter issimple="1">
<name>T</name>
<prompt lang="en">Temperature (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>
<ctrl>
<message>
<text lang="en">Enter a value between 0 and 100</text>
</message>
<code proglang="perl">$value <= 100 and $value >= 0</code>
<code proglang="python">value <= 100 and value >= 0</code>
</ctrl>
<argpos>3</argpos>
</parameter>
<parameter>
<name>P</name>
<prompt lang="en">Percent (P)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>5</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " P=$value" : ""</code>
<code proglang="python">("", " P="+str(value))[value is not None and value != vdef]</code>
</format>
<argpos>3</argpos>
<comment>
<text lang="en">This is the percent suboptimality for computing the energy dot plot and suboptimal foldings. The default value is 5%. This parameter controls the value of the free energy increment, delta (deltaG). Delta of deltaG is set to P% of deltaG, computed minimum free energy. The energy dot plot shows only those base pairs that are in foldings with free energy minus or equal to deltaG plus delta (deltaG). Similarly, the free energies of computed foldings are in the range from deltaG to deltaG plus delta (deltaG). No matter the value of P, mfold currently keeps delta (deltaG) in the range [1,12] (kcal/mole).</text>
</comment>
</parameter>
<parameter issimple="1">
<name>NA_CONC</name>
<prompt lang="en">Na+ molar concentration (NA_CONC)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>1.0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " NA_CONC=$value" : ""</code>
<code proglang="python">("" , " NA_CONC=" + str(value))[ value is not None and value != vdef]</code>
</format>
<argpos>3</argpos>
</parameter>
<parameter issimple="1">
<name>MG_CONC</name>
<prompt lang="en">Mg++ molar concentration (MG_CONC)</prompt>
<type>
<datatype>
<class>Float</class>
</datatype>
</type>
<vdef>
<value>0.0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " MG_CONC=$value" : ""</code>
<code proglang="python">("" , " MG_CONC=" + str(value))[ value is not None and value != vdef]</code>
</format>
<argpos>3</argpos>
</parameter>
<parameter>
<name>W</name>
<prompt lang="en">Window parameter (W)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " W=$value" : ""</code>
<code proglang="python">("" , " W=" + str(value))[ value is not None ]</code>
</format>
<argpos>3</argpos>
<comment>
<text lang="en">This is the window parameter that controls the number of foldings that are automatically computed by mfold . `W' may be thought of as a distance parameter. The distance between 2 base pairs, i.j and i'.j' may be defined as max{|i-i'|,|j-j'|}. Then if k-1 foldings have already been predicted by mfold , the kth folding will have at least W base pairs that are at least a distance W from any of the base pairs in the first k-1 foldings. As W increases, the number of predicted foldings decreases. If W is not specified, mfold selects a value by default based on sequence length.</text>
</comment>
</parameter>
<parameter>
<name>MAXBP</name>
<prompt lang="en">Max base pair distance (MAXBP)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " MAXBP=$value" : ""</code>
<code proglang="python">("" , " MAXBP=" + str(value))[ value is not None ]</code>
</format>
<argpos>3</argpos>
<comment>
<text lang="en">A base pair i.j will not be allowed to form (in linear RNA) if j-i > MAXBP. For circular RNA, a base pair i.j cannot form if min{j-i,n+i-j} > MAXBP . Thus small values of MAXBP ensure that only short range base pairs will be predicted. By default, MAXBP=+infinity, indicating no constraint. </text>
</comment>
</parameter>
<parameter>
<name>MAX_LP</name>
<prompt lang="en">Maximum bulge/interior loop size (MAX_LP)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>30</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " MAX_LP=$value" : ""</code>
<code proglang="python">("" , " MAX_LP=" + str(value))[ value is not None and value != vdef]</code>
</format>
<argpos>3</argpos>
</parameter>
<parameter>
<name>MAX_AS</name>
<prompt lang="en">Maximum asymmetry of a bulge/interior loop (MAX_AS)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>30</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " MAX_AS=$value" : ""</code>
<code proglang="python">("" , " MAX_AS=" + str(value))[ value is not None and value != vdef]</code>
</format>
<argpos>3</argpos>
</parameter>
<parameter>
<name>MAX</name>
<prompt lang="en">Maximum number of foldings to be computed (MAX)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>50</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " MAX=$value" : ""</code>
<code proglang="python">("" , " MAX=" + str(value))[ value is not None and value != vdef]</code>
</format>
<argpos>3</argpos>
<comment>
<text lang="en">MAX : This is the maximum number of foldings that mfold will compute (50 by default). It is better to limit the number of foldings by careful selection of the P and W parameters. </text>
</comment>
</parameter>
<parameter>
<name>ANN</name>
<prompt lang="en">Structure annotation type (ANN)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>none</value>
</vdef>
<vlist>
<velem>
<value>none</value>
<label>No special annotation</label>
</velem>
<velem>
<value>p-num</value>
<label>p-num</label>
</velem>
<velem>
<value>ss-count</value>
<label>ss-count</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " ANN=$value" : ""</code>
<code proglang="python">("" , " ANN=" + str(value))[ value is not None and value != vdef]</code>
</format>
<argpos>2</argpos>
<comment>
<text lang="en">This parameter currently takes on 3 values. </text>
<text lang="en">- `none' : secondary structures are drawn without any special annotation. Letters or outline are in black, while base pairs are red lines or dots for GC pairs and blue lines or dots for AU and GU pairs. </text>
<text lang="en">- `p-num' : Colored dots, colored base characters or a combination are used to display in each folding how well-determined each base is according to the P-num values in the `fold_name.ann' file. </text>
<text lang="en">- `ss-count' : Colored dots, colored base characters or a combination are used to display in each folding how likely a base is to be single-stranded according to sample statistics stored in the `fold_name.ss-count' file.</text>
</comment>
</parameter>
<parameter>
<name>MODE</name>
<prompt lang="en">Structure display mode (MODE)</prompt>
<type>
<datatype>
<class>Choice</class>
</datatype>
</type>
<vdef>
<value>auto</value>
</vdef>
<vlist>
<velem>
<value>auto</value>
<label>Auto</label>
</velem>
<velem>
<value>bases</value>
<label>Bases</label>
</velem>
<velem>
<value>lines</value>
<label>Lines</label>
</velem>
</vlist>
<format>
<code proglang="perl">(defined $value and $value ne $vdef) ? " MODE=$value" : ""</code>
<code proglang="python">("" , " MODE=" + str(value))[ value is not None and value != vdef]</code>
</format>
<argpos>2</argpos>
</parameter>
<parameter>
<name>ROT_ANG</name>
<prompt lang="en">Structure rotation angle (ROT_ANG)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " ROT_ANG=$value" : ""</code>
<code proglang="python">("" , " ROT_ANG=" + str(value))[ value is not None and value != vdef]</code>
</format>
<argpos>3</argpos>
</parameter>
<parameter>
<name>START</name>
<prompt lang="en">5' base number (START)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">(defined $value and $value != $vdef) ? " START=$value" : ""</code>
<code proglang="python">("" , " START=" + str(value))[ value is not None and value != vdef]</code>
</format>
<argpos>3</argpos>
</parameter>
<parameter>
<name>STOP</name>
<prompt lang="en">3' base number (STOP)</prompt>
<type>
<datatype>
<class>Integer</class>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " STOP=$value" : ""</code>
<code proglang="python">("" , " STOP=" + str(value))[ value is not None ]</code>
</format>
<argpos>3</argpos>
</parameter>
<parameter>
<name>AUX</name>
<prompt lang="en">Constraints File (AUX)</prompt>
<type>
<datatype>
<class>MfoldFoldingConstraints</class>
<superclass>AbstractText</superclass>
</datatype>
</type>
<format>
<code proglang="perl">(defined $value) ? " AUX=$value" : ""</code>
<code proglang="python">( "" , " AUX=" + str(value) )[ value is not None]</code>
</format>
<argpos>3</argpos>
<comment>
<text lang="en">
AUX : (optional) This is the name of an auxiliary input file of folding
constraints. If this parameter is not used, mfold looks for a file
named `fold_name.aux'. If this file exists and is not empty, then it
is interpreted as a constraint file. Thus constraints may be used
without the use of this command line parameter.</text>
<text lang="en">Fill the box or the file with constraints (1 constraint per line) You may:</text>
<text lang="en"> 1. force bases i,i+1,...,i+k-1 to be double stranded by entering:</text>
<text lang="en"> F i 0 k </text>
<text lang="en"> 2. force consecutive base pairs i.j,i+1.j-1, ...,i+k-1.j-k+1 by entering:</text>
<text lang="en"> F i j k </text>
<text lang="en"> 3. force bases i,i+1,...,i+k-1 to be single stranded by entering:</text>
<text lang="en"> P i 0 k </text>
<text lang="en"> 4. prohibit the consecutive base pairs</text>
<text lang="en"> i.j,i+1.j-1, ...,i+k-1.j-k+1 by entering:</text>
<text lang="en"> P i j k </text>
<text lang="en"> 5. prohibit bases i to j from pairing with bases k to l by entering:</text>
<text lang="en"> P i-j k-l </text>
</comment>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>runtype</name>
<prompt lang="en">Output options</prompt>
<argpos>3</argpos>
<parameters>
<parameter>
<name>txt_format</name>
<prompt lang="en">Text output file</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>1</value>
</vdef>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
<argpos>4</argpos>
</parameter>
<parameter isstdout="1">
<name>txt_out</name>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<precond>
<code proglang="perl">$txt_format</code>
<code proglang="python">txt_format</code>
</precond>
<filenames>
<code proglang="perl">"*.out"</code>
<code proglang="python">"*.out"</code>
</filenames>
</parameter>
<parameter>
<name>det_format</name>
<prompt lang="en">Detailed output file</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">""</code>
<code proglang="python">""</code>
</format>
<argpos>4</argpos>
</parameter>
<parameter isout="1">
<name>det_out_html</name>
<prompt>Detailed outfile</prompt>
<type>
<datatype>
<class>MfoldDetailHtmlReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$det_format and $html_format </code>
<code proglang="python">det_format and html_format </code>
</precond>
<filenames>
<code proglang="perl">"*.det.html"</code>
<code proglang="python">"*.det.html"</code>
</filenames>
</parameter>
<parameter isout="1">
<name>det_out</name>
<prompt>Detailed outfile</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<precond>
<code proglang="perl">$det_format and not $html_format </code>
<code proglang="python">det_format and not html_format </code>
</precond>
<filenames>
<code proglang="perl">"*.det"</code>
<code proglang="python">"*.det"</code>
</filenames>
</parameter>
<parameter>
<name>html_format</name>
<prompt lang="en">Html output file</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<format>
<code proglang="perl">($value) ? " RUN_TYPE=html" : ""</code>
<code proglang="python">("" , " RUN_TYPE=html")[ value ]</code>
</format>
<argpos>4</argpos>
</parameter>
<parameter isout="1">
<name>out_html</name>
<prompt lang="en">Html output file</prompt>
<type>
<datatype>
<class>MfoldHtmlReport</class>
<superclass>Report</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$html_format</code>
<code proglang="python">html_format</code>
</precond>
<filenames>
<code proglang="perl">"*.html"</code>
<code proglang="python">"*.html"</code>
</filenames>
</parameter>
<parameter>
<name>rnaml_format</name>
<prompt lang="en">RNAML output file</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<comment>
<text lang="en">The RNAML (RNA Markup Language) was developed by a consortium of investigators and is a proposed syntax for RNA information files. A description was published in 2002:
</text>
<text lang="en">A. Waugh, P. Gendron, R. Altman, J.W. Brown, D. Case, D. Gautheret, S.C. Harvey, N. Leontis, J. Westbrook, E. Westhof, M. Zuker, and
F. Major RNAML: A standard syntax for exchanging RNA information. RNA 8 (6), 707-717, (2002)</text>
</comment>
</parameter>
<parameter isout="1">
<name>out_rnaml</name>
<prompt lang="en">RNAML output file</prompt>
<type>
<biotype>RNA</biotype>
<datatype>
<class>2DStructure</class>
<superclass>AbstractText</superclass>
</datatype>
<dataFormat>RNAML</dataFormat>
</type>
<precond>
<code proglang="perl">$rnaml_format </code>
<code proglang="python">rnaml_format </code>
</precond>
<filenames>
<code proglang="perl">"*.rnaml"</code>
<code proglang="python">"*.rnaml"</code>
</filenames>
</parameter>
<paragraph>
<name>energy_param</name>
<prompt lang="en">Energy Dot plot</prompt>
<argpos>3</argpos>
<parameters>
<parameter>
<name>plot_format</name>
<prompt lang="en">Energy dot plot output file</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<comment>
<text lang="en">This is a text file that contains all the
base pairs on the energy dot plot , organized into helices for which Delta G(i,j) is constant. The first record is a header, and each subsequent record
describes a single helix. The records are usually sorted by Delta G(i,j) and are often filtered so that short helices or isolated base pairs (helices of length 1) in suboptimal foldings are removed.</text>
</comment>
</parameter>
<parameter isout="1">
<name>out_plot</name>
<prompt lang="en">Energy dot plot output file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<precond>
<code proglang="perl">$plot_format</code>
<code proglang="python">plot_format</code>
</precond>
<filenames>
<code proglang="perl">"*.plot"</code>
<code proglang="python">"*.plot"</code>
</filenames>
</parameter>
<parameter>
<name>ann_format</name>
<prompt lang="en">Structure annotation output file</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
</parameter>
<parameter isout="1">
<name>ann_plot</name>
<prompt lang="en">Structure annotation output file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<precond>
<code proglang="perl">$ann_format</code>
<code proglang="python">ann_format</code>
</precond>
<filenames>
<code proglang="perl">"*.ann"</code>
<code proglang="python">"*.ann"</code>
</filenames>
</parameter>
<parameter>
<name>hnum_format</name>
<prompt lang="en">Helix num output file</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<comment>
<text lang="en">This file is the same as plot file, except that the energy column is replaced by an h-num column. These files are usually sorted by h-num; lowest to highest, or best determined to worst determined. Often, only helices in optimal foldings are retained.</text>
</comment>
</parameter>
<parameter isout="1">
<name>hnum_plot</name>
<prompt lang="en">Helix num output file</prompt>
<type>
<datatype>
<class>Text</class>
</datatype>
</type>
<precond>
<code proglang="perl">$hnum_format</code>
<code proglang="python">hnum_format</code>
</precond>
<filenames>
<code proglang="perl">"*.h-num"</code>
<code proglang="python">"*.h-num"</code>
</filenames>
</parameter>
</parameters>
</paragraph>
<paragraph>
<name>structure_format</name>
<prompt lang="en">Structure file format</prompt>
<argpos>3</argpos>
<parameters>
<parameter>
<name>gif_format</name>
<prompt lang="en">GIF output file</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<comment>
<text lang="en">A graphics file that ends with the suffix .gif should be displayed directly on the page of your web browser.</text>
</comment>
</parameter>
<parameter isout="1">
<name>out_gif</name>
<prompt lang="en">GIF output file</prompt>
<type>
<datatype>
<class>Picture</class>
<superclass>Binary</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$gif_format</code>
<code proglang="python">gif_format</code>
</precond>
<filenames>
<code proglang="perl">*.gif</code>
<code proglang="python">"*.gif"</code>
</filenames>
</parameter>
<parameter>
<name>pdf_format</name>
<prompt lang="en">PDF output file</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
</parameter>
<parameter isout="1">
<name>out_pdf</name>
<prompt lang="en">PDF output file</prompt>
<type>
<datatype>
<class>Pdf</class>
<superclass>Binary</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$pdf_format</code>
<code proglang="python">pdf_format</code>
</precond>
<filenames>
<code proglang="perl">"*.pdf"</code>
<code proglang="python">"*.pdf"</code>
</filenames>
</parameter>
<parameter>
<name>ps_format</name>
<prompt lang="en">Postscript output file</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<comment>
<text lang="en">PostScript is a programming language that is used to describe output for printing and display. It was developed by Adobe Systems. It is common to have PostScript capability on most printers. Programs such as Ghostscript, Ghostview and GSview can be used to display PostScript files(http://www.cs.wisc.edu/~ghost/").</text>
</comment>
</parameter>
<parameter isout="1">
<name>out_ps</name>
<prompt lang="en">Postscript output file</prompt>
<type>
<datatype>
<class>PostScript</class>
<superclass>Binary</superclass>
</datatype>
</type>
<precond>
<code proglang="perl">$ps_format</code>
<code proglang="python">ps_format</code>
</precond>
<filenames>
<code proglang="perl">"*.ps"</code>
<code proglang="python">"*.ps"</code>
</filenames>
</parameter>
<parameter>
<name>ct_format</name>
<prompt lang="en">CT output file</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<comment>
<text lang="en">The '.ct file' contains the nucleic acid sequence and base pairing information from which a structure plot may be computed. The mfold software and mfold web servers use the "sir_graph_ng" program to create Postscript, jpg and png images from .ct files. "sir_graph_ng" is part of the mfold_util package that may be obtained here: http://www.bioinfo.rpi.edu/~zukerm/export/.</text>
</comment>
</parameter>
<parameter isout="1">
<name>out_ct</name>
<prompt lang="en">CT output file</prompt>
<type>
<datatype>
<class>2DStructure</class>
<superclass>AbstractText</superclass>
</datatype>
<dataFormat>CT</dataFormat>
</type>
<precond>
<code proglang="perl">$ct_format</code>
<code proglang="python">ct_format</code>
</precond>
<filenames>
<code proglang="perl">"*.ct"</code>
<code proglang="python">"*.ct"</code>
</filenames>
</parameter>
<parameter>
<name>ss_format</name>
<prompt lang="en">XRNA_ss output file</prompt>
<type>
<datatype>
<class>Boolean</class>
</datatype>
</type>
<vdef>
<value>0</value>
</vdef>
<comment>
<text lang="en">This is an input file for the XRNA program by Bryn Weiser and Harry Noller.
The new Java version is available from UC Santa Cruz RNA Center web site:
href="http://rna.ucsc.edu/rnacenter/xrna/xrna.html". The
ss file can be regarded as an expanded ct file. It contains base and connect information as
well a coordinates for plotting the bases.</text>
</comment>
</parameter>
<parameter isout="1">
<name>out_ss</name>
<prompt lang="en">XRNA_ss output file</prompt>
<type>
<datatype>
<class>2DStructure</class>
<superclass>AbstractText</superclass>
</datatype>
<dataFormat>SS</dataFormat>
</type>
<precond>
<code proglang="perl">$ss_format</code>
<code proglang="python">ss_format</code>
</precond>
<filenames>
<code proglang="perl">"*.ss"</code>
<code proglang="perl">"*.ss-count"</code>
<code proglang="python">"*.ss"</code>
<code proglang="python">"*.ss-count"</code>
</filenames>
</parameter>
</parameters>
</paragraph>
</parameters>
</paragraph>
</parameters>
</program>
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