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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN"><!--Converted with LaTeX2HTML 98.1p1 release (March 2nd, 1998)originally by Nikos Drakos (nikos@cbl.leeds.ac.uk), CBLU, University of Leeds* revised and updated by:  Marcus Hennecke, Ross Moore, Herb Swan* with significant contributions from:  Jens Lippmann, Marek Rouchal, Martin Wilck and others --><HTML><HEAD><TITLE>AUXILIARY AND INDIVIDUAL PROGRAMS</TITLE><META NAME="description" CONTENT="AUXILIARY AND INDIVIDUAL PROGRAMS"><META NAME="keywords" CONTENT="FEBS98-html"><META NAME="resource-type" CONTENT="document"><META NAME="distribution" CONTENT="global"><META HTTP-EQUIV="Content-Type" CONTENT="text/html; charset=iso-8859-1"><LINK REL="STYLESHEET" HREF="FEBS98-html.css"><LINK REL="previous" HREF="node9.html"><LINK REL="up" HREF="node7.html"><LINK REL="next" HREF="node13.html"></HEAD><BODY BGCOLOR=#FFDEAD TEXT=#202020 LINK=#800000 ALINK=#ffff00 VLINK=#353976><!--Navigation Panel--><A NAME="tex2html193" HREF="node13.html"><IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="img/next_motif.gif"></A> <A NAME="tex2html190" HREF="node7.html"><IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="img/up_motif.gif"></A> <A NAME="tex2html186" HREF="node11.html"><IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="img/previous_motif.gif"></A> <A NAME="tex2html192" HREF="node1.html"><IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents" SRC="img/contents_motif.gif"></A>  <BR><B> Next:</B> <A NAME="tex2html194" HREF="node13.html">Sample foldings</A><B> Up:</B> <A NAME="tex2html191" HREF="node7.html">Running the programs</A><B> Previous:</B> <A NAME="tex2html187" HREF="node11.html">Optimal and suboptimal foldings</A><BR><BR><!--End of Navigation Panel--><H2><A NAME="SECTION00073000000000000000"> <SMALL>AUXILIARY AND INDIVIDUAL PROGRAMS</SMALL></A></H2><P>The <I>mfold</I> package contains a script, also named <I>mfold</I> , that performsa folding according to information entered on the command line. Thisscript is itself composed of scripts and (Fortran or C) executableprograms, many of which can be run separately. Some of these programsare now described.<P><DL COMPACT><DD><P><DT>1.<DD><I>auxgen</I>: This program creates the  `<SMALL>FILE_NAME.PNT'</SMALL> file. <P><DT>2.<DD><I>boxplot97_ng</I>: This program creates an <I>energy dot plot</I> in PostScript orgif form from  `<SMALL>FILE_NAME.PLOT'</SMALL>. The file  <SMALL>BOXPLOT97_NG.DOC</SMALL>contains instructions. <P><DT>3.<DD><I>ct_boxplot</I>: This program creates a dot plot containingonly those base pairs found in a collection of structures (in ``ctformat'') that are specified on the command line. These must all befoldings of the same sequence fragment. At present, the <I>mfold</I> scriptdoes not use this program.<P><DT>4.<DD><I>ct_compare</I>: This program compares 2 ``ct files''. Thefirst contains a single reference structure. The second contains 1 ormore foldings of the same sequence. The number of bases and helicesfrom the first structure that are conserved in the other structuresare computed and displayed. For the purposes of this program, a``helix'' may contain bulge or interior loops of size 1 or 2 and musthave at least 3 base pairs [<A HREF="node19.html#JAEJ8901">17</A>,<A HREF="node19.html#ZUKM9102">40</A>].<P><DT>5.<DD><I>efn</I>: This program computes <IMG WIDTH="29" HEIGHT="15" ALIGN="BOTTOM" BORDER="0" SRC="img6.gif" ALT="$\Delta G$">for all the foldings in a``ct file''. The energy rules correspond exactly to what is used in <I>mfold</I> . <DT>6.<DD><I>efn2</I>: This program computes <IMG WIDTH="29" HEIGHT="15" ALIGN="BOTTOM" BORDER="0" SRC="img6.gif" ALT="$\Delta G$">for all the foldings ina ``ct file'' using a more precise free energy computation that takesinto account coaxial stacking and Jacobson-Stockmeyer theory formulti-branched loops. (See equation <A HREF="node5.html#DDGM2">7</A> and Figure <A HREF="node5.html#COAX">8</A>,respectively.)<P><DT>7.<DD><I>h-num</I>: This program computes an ``h-num'' file from a``plot'' file.<P><DT>8.<DD><I>nafold</I>: This is the principle folding program of the<I>mfold</I> package, and corresponds to the program ``lrna'' and ``crna''in earlier versions of <I>mfold</I> . It has 2 command line arguments. Thefirst takes on the values `l' or `c', for linear (default) orcircular folding, respectively. The second has values ``text''(default) or ``html'' for plain text output, and for some htmloutput, as described above. It is run twice by the <I>mfold</I> script. Itmay be run alone, as it prompts the user for input on an interactivebasis. In this mode, the user may fold all the sequences contained ina single file, an option not available with the <I>mfold</I> script. Theinstructions for running this program have been described in[<A  HREF="node19.html#ZUKM9401">19</A>] and also on the WWW at <TT>http://www.bioinfo.rpi.edu/<code>~</code>zukerm/mfold-2.0</TT>. The interactive <I>energy dot plot</I> is not functional in version 3.0.<P><DT>9.<DD><I>naview</I>: This is a modified version of the <I>naview</I>program described in [<A HREF="node19.html#BRUR8801">41</A>]. Actually, in <I>mfold</I> , <I>naview</I> is a script that runs a binary called <I>naview.exe</I>.  Both<I>naview</I> and <I>naview.exe</I> may be run alone in interactiveform.  The <I>mfold</I> script uses the files ``bases.nav'' and``lines.nav'', stored in <I>MFOLDLIB</I> to direct ``naview''. Thefirst produces an output that displays individual residues as letters,while the second gives a structure outline only.<P><DT>10.<DD><I>newtemp</I>: The <I>newtemp</I> program creates free energyfiles for folding RNA or DNA at different temperatures. The latest RNAparameters consist only of free energies measured at 37&#176;.Since there are no corresponding enthalpy files, it is not possible tofold RNA at temperatures other than 37&#176;.If the user wishesto fold RNA at different temperatures, then the ``dg'' and ``dh''files from <I>mfold</I> version 2.3 should be copied into <I>MFOLDLIB</I>. These older free energy parameters will be supplied with<I>mfold</I> version 3.0. DNA folding may be done at arbitrary temperaturesbetween 0 and 100 degrees. However, it should be remembered that theDNA loop parameters are all estimated from values published in theliterature or by comparison with RNA.<P><DT>11.<DD><I>plt22ps</I>: This program takes a ``plt2'' file from <I>naview</I> and creates a PostScript file of a plotted structure. It canuse an ``ann'' file or an ``ss-count'' file to annotate with P-num orss-count values, respectively.<P><DT>12.<DD><I>plt22gif</I>: This program is the same as <I>plt22ps</I>,except that the structure output file is in gif format.<P><DT>13.<DD><I>sav2p-num</I>: This interactive program uses an existing `fold_name.sav' file to create a P-num file.<P><DT>14.<DD><I>sav2plot</I>: This interactive program uses an existing `fold_name.sav' file to create a ``plot'' file. The resulting``plot'' file may be sorted and filtered using the command: <SMALL>FILTER-SORT NAME.PLOT N</SMALL>, where name.plot is a ``plot'' file, and <SMALL>N</SMALL> is the minimum helix size that is desired. Helices shorter than <SMALL>N</SMALL> and not removed in optimal foldings.<P><DT>15.<DD><I>scorer</I>: This program is similar to <I>ct_compare</I>. Itcompares foldings helix by helix, displaying  a more detailed output.<P><DT>16.<DD><I>split_ct.awk</I>: This is a Unix awk script that splits a ctfile into multiple files, containing 1 folding in each. Theseindividual files may be processed by <I>naview</I>, <I>plt22ps</I> and<I>plt22gif</I>. <P><DT>17.<DD><I>ss-count</I>: This program computes single stranded samplestatistics from a collection of foldings stored in a single ct file.<P></DL><P><HR><!--Navigation Panel--><A NAME="tex2html193" HREF="node13.html"><IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="img/next_motif.gif"></A> <A NAME="tex2html190" HREF="node7.html"><IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="img/up_motif.gif"></A> <A NAME="tex2html186" HREF="node11.html"><IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="img/previous_motif.gif"></A> <A NAME="tex2html192" HREF="node1.html"><IMG WIDTH="65" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="contents" SRC="img/contents_motif.gif"></A>  <BR><B> Next:</B> <A NAME="tex2html194" HREF="node13.html">Sample foldings</A><B> Up:</B> <A NAME="tex2html191" HREF="node7.html">Running the programs</A><B> Previous:</B> <A NAME="tex2html187" HREF="node11.html">Optimal and suboptimal foldings</A><!--End of Navigation Panel--><ADDRESS><TABLE><TR><TD><IMG SRC=img/shield16.gif HSPACE=20></TD><TD><I>Michael Zuker <BR>Institute for Biomedical Computing<BR>Washington University in St. Louis<BR>1998-12-05</I></TD></TR></TABLE></ADDRESS></BODY></HTML>
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