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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>Abstract</TITLE><META NAME="description" CONTENT="Abstract"><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="node3.html"><LINK REL="previous" HREF="node1.html"><LINK REL="up" HREF="FEBS98-html.html"><LINK REL="next" HREF="node3.html"></HEAD><BODY BGCOLOR=#FFDEAD TEXT=#202020 LINK=#800000 ALINK=#ffff00 VLINK=#353976><!--Navigation Panel--><A NAME="tex2html80" HREF="node3.html"><IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="img/next_motif.gif"></A> <A NAME="tex2html77" HREF="FEBS98-html.html"><IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="img/up_motif.gif"></A> <A NAME="tex2html71" HREF="node1.html"><IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="img/previous_motif.gif"></A> <A NAME="tex2html79" 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="tex2html81" HREF="node3.html">Introduction</A><B> Up:</B> <A NAME="tex2html78" HREF="FEBS98-html.html">Algorithms and Thermodynamics for</A><B> Previous:</B> <A NAME="tex2html72" HREF="node1.html">Contents</A><BR><BR><!--End of Navigation Panel--><H1><A NAME="SECTION00020000000000000000">Abstract</A></H1><P><IMG SRC="img/t.gif">his article is about the current status of the <I>mfold</I> package for RNAand DNA secondary structure prediction using nearest neighborthermodynamic rules. The details of the free energy rules and of thelatest version 3.0 software are described. Future plans are alsodiscussed.<P>The <I>mfold</I> software now runs on a variety of Unix platforms;specifically SGI Irix, Sun Solaris, Dec alpha Ultrix and onLinux. While the older interactive programs of version 2 still exist,they are now run by a variety of scripts that make for much easierhandling. There is both a command line interface for <I>mfold</I> andan HTML interface that runs in a Unix environment but can be accessedby anyone with a web browser.<P>The thermodynamic basis for the folding model is presented in detail,with references given for both specific free energy parameters and tooverview articles that have summarized the state of these nearestneighbor parameters over the past dozen years. Both RNA and DNA rulesare discussed, with some mention of parameters for RNA/DNAhybridization. Although the thermodynamic model has grown incomplexity to accommodate new types of information, the foldingalgorithm has not yet incorporated some features, such as coaxialstacking of adjacent helices, and other features will probably remaintoo difficult or computationally expensive to implement. For thisreason, a new energy calculation program has been introduced torecompute the free energies of predicted foldings to reflect the bestof our knowledge.<P>The most significant improvements in the <I>mfold</I> software are:<DL COMPACT><FONT COLOR="#8B1A1A"><DT>1.<DD>Folding times have been greatly reduced in recent years, partlybecause of faster computers and partly because of improvements in thealgorithm. <DT>2.<DD>Folding constraints have been expanded and are now implementedwithout the use of <I>bonus energies</I> that distort the results.<DT>3.<DD>The output is significantly improved. Clear and enlargeableimages of <I>dot plots</I> and of predicted foldings are now producedin PostScript and <I>gif</I> formats. Bases in structures may beannotated using different colors that reflect how <I>well-determined</I>they are in terms of their tendency to pair with other bases or to besingle-stranded. Similarly, base pair probabilities from partitionfunction calculations may be used for annotation. A detaileddecomposition of each predicted folding into stacked pairs and loopswith associated free energies is now provided.</DL></FONT><P>The <I>mfold</I> software has a variety of parameters that may beadjusted to improve the predictions. Several examples arepresented to illustrate how to interpret folding results and how toadjust these parameters to obtain better results.<P><HR><!--Navigation Panel--><A NAME="tex2html80" HREF="node3.html"><IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="img/next_motif.gif"></A> <A NAME="tex2html77" HREF="FEBS98-html.html"><IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="img/up_motif.gif"></A> <A NAME="tex2html71" HREF="node1.html"><IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="img/previous_motif.gif"></A> <A NAME="tex2html79" 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="tex2html81" HREF="node3.html">Introduction</A><B> Up:</B> <A NAME="tex2html78" HREF="FEBS98-html.html">Algorithms and Thermodynamics for</A><B> Previous:</B> <A NAME="tex2html72" HREF="node1.html">Contents</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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