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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>Future plans</TITLE><META NAME="description" CONTENT="Future plans"><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="next" HREF="node18.html"><LINK REL="previous" HREF="node13.html"><LINK REL="up" HREF="FEBS98-html.html"><LINK REL="next" HREF="node18.html"></HEAD><BODY BGCOLOR=#FFDEAD TEXT=#202020 LINK=#800000 ALINK=#ffff00 VLINK=#353976><!--Navigation Panel--><A NAME="tex2html249" HREF="node18.html"><IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="img/next_motif.gif"></A> <A NAME="tex2html246" HREF="FEBS98-html.html"><IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="img/up_motif.gif"></A> <A NAME="tex2html240" HREF="node16.html"><IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="img/previous_motif.gif"></A> <A NAME="tex2html248" 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="tex2html250" HREF="node18.html">Acknowledgment</A><B> Up:</B> <A NAME="tex2html247" HREF="FEBS98-html.html">Algorithms and Thermodynamics for</A><B> Previous:</B> <A NAME="tex2html241" HREF="node16.html">EXAMPLE 3</A><BR><BR><!--End of Navigation Panel--><H1><A NAME="SECTION00090000000000000000">Future plans</A></H1><P>The Unix version of <I>mfold</I> will remain. The newest programs, such as<I>plt22ps</I> and <I>plt22gif</I> are written in command linemode. The older programs have shell scripts or Perl ``wrappers''around them to make them appear as single binaries that operate incommand line mode. The trend will be to replace older code asnecessary with non-interactive programs. This makes it easier to piecetogether different programs to create new forms of output.<P>When <I>mfold</I> was first created, the limitations of personal computersdid not make a PC version practical. This has changed radically in thepast 10 years, and an Intel/Windows PC is now a fine environment forrunning <I>mfold</I> . The basic Fortran and C programs have already beenported and will run under Widows, but a Unix-like shell isnecessary. The <I>RNAstructure</I> program is now a faithful recreationof <I>mfold</I> in Windows, with a convenient user interface. The majorproblem with the existing setup is that the Unix and Windows versionsare totally different and will have to be updated in parallel to keepthem equivalent.<P>The <I>mfold</I> programs running on SGI/Irix, SPARC/Solaris andIntel/Solaris have been incorporated into a world wide web (WWW)server that allows users from around the world to submit sequences forfolding. This server has some extra features not available in the<I>mfold</I> package, and goes well beyond the very simple HTML output ofthe current <I>mfold</I> software. However, this software offers nothing newin terms of predictions, and it will be described elsewhere. Rapiddevelopments in web browsers and languages such as Java-script and Javamay make an HTML (or similar) interface to <I>mfold</I> better thanothers. As things stand now, the <I>mfold</I> server can run on a (local)Unix computer and be accessed by web browsers running on personalcomputers. <P>Additional parameters will be added to the command line version of<I>mfold</I> in the future. These will be described when the <I>mfold</I> commandis given without parameters and the documentation will be alteredaccordingly. In the near future, a base labeling frequency will beadded so that the user can specify the frequency of baseenumeration. Other controls on secondary structure, such as zooming onimages about specified coordinates, could be added, but these are already available through the use of the <I>plt22ps</I> and<I>plt22gif</I> programs.<P>The ``energy'' parameters from the older, interactive versions of<I>mfold</I> could easily be introduced in command line form. This wouldmake it unnecessary to run the <I>nafold</I> program directly to alterthem. Table <A HREF="#EPARAMS">5</A> lists these parameters that are not definedin the <SMALL>MISCLOOP</SMALL> file.<P><BR><DIV ALIGN="CENTER"><A NAME="850"> </A><TABLE><CAPTION><STRONG>Table 5:</STRONG>Additional command line variables that couldbe added to <I> mfold</I> .</CAPTION><TR><TD><TABLE CELLPADDING=3 BORDER="1"><TR><TD ALIGN="LEFT"><B> Parameter</B></TD><TD ALIGN="LEFT"><B> Description</B></TD><TD ALIGN="CENTER"><B> Default value</B></TD></TR><TR><TD ALIGN="LEFT">ddSTACK</TD><TD ALIGN="LEFT">extra <!-- MATH: $\delta \delta G$ --><IMG WIDTH="31" HEIGHT="15" ALIGN="BOTTOM" BORDER="0" SRC="img27.gif" ALT="$\delta \delta G$">per stack</TD><TD ALIGN="CENTER">0</TD></TR><TR><TD ALIGN="LEFT">ddBULGE</TD><TD ALIGN="LEFT">extra <!-- MATH: $\delta \delta G$ --><IMG WIDTH="31" HEIGHT="15" ALIGN="BOTTOM" BORDER="0" SRC="img27.gif" ALT="$\delta \delta G$">per bulge loop</TD><TD ALIGN="CENTER">0</TD></TR><TR><TD ALIGN="LEFT">ddILOOP</TD><TD ALIGN="LEFT">extra <!-- MATH: $\delta \delta G$ --><IMG WIDTH="31" HEIGHT="15" ALIGN="BOTTOM" BORDER="0" SRC="img27.gif" ALT="$\delta \delta G$">per interior loop</TD><TD ALIGN="CENTER">0</TD></TR><TR><TD ALIGN="LEFT">ddHLOOP</TD><TD ALIGN="LEFT">extra <!-- MATH: $\delta \delta G$ --><IMG WIDTH="31" HEIGHT="15" ALIGN="BOTTOM" BORDER="0" SRC="img27.gif" ALT="$\delta \delta G$">per hairpin loop</TD><TD ALIGN="CENTER">0</TD></TR><TR><TD ALIGN="LEFT">MAXILOOP</TD><TD ALIGN="LEFT">maximum size of an internal loop</TD><TD ALIGN="CENTER">30</TD></TR><TR><TD ALIGN="LEFT">MAXLOP</TD><TD ALIGN="LEFT">maximum asymmetry of an internal loop</TD><TD ALIGN="CENTER">30</TD></TR></TABLE></TD></TR></TABLE></DIV><BR><P>Current plans call for the addition of coaxial stacking to the foldingalgorithm and possibly the creation of a special version that usesJacobson-Stockmeyer theory to assign more realistic free energies tomulti-branch loops, as in equation <A HREF="node5.html#DDGM2">7</A>. In addition, apractical approach to pseudoknots will be attempted, where pairs ofmutually exclusive helices that create pseudoknots are identified inthe <I>energy dot plot</I> . In these case, the bases involved in 1 or perhaps 2 of thesepseudoknots can be constrained to be single stranded, and foldingspredicted to fill in the rest of the secondary structure.<P>Another future development will be the introduction of a 2 moleculefolding system. This immediately complicates the problem, sinceconcentration now becomes important. In addition, the folding ofcertain very simple bi-molecular systems is at least as hard aspredicting pseudoknots in the folding of a single sequence.<P><HR><!--Navigation Panel--><A NAME="tex2html249" HREF="node18.html"><IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="img/next_motif.gif"></A> <A NAME="tex2html246" HREF="FEBS98-html.html"><IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="img/up_motif.gif"></A> <A NAME="tex2html240" HREF="node16.html"><IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="img/previous_motif.gif"></A> <A NAME="tex2html248" 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="tex2html250" HREF="node18.html">Acknowledgment</A><B> Up:</B> <A NAME="tex2html247" HREF="FEBS98-html.html">Algorithms and Thermodynamics for</A><B> Previous:</B> <A NAME="tex2html241" HREF="node16.html">EXAMPLE 3</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>⌨️ 快捷键说明
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