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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>EXAMPLE 1</TITLE><META NAME="description" CONTENT="EXAMPLE 1"><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="node15.html"><LINK REL="previous" HREF="node13.html"><LINK REL="up" HREF="node13.html"><LINK REL="next" HREF="node15.html"></HEAD><BODY BGCOLOR=#FFDEAD TEXT=#202020 LINK=#800000 ALINK=#ffff00 VLINK=#353976><!--Navigation Panel--><A NAME="tex2html218" HREF="node15.html"><IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="img/next_motif.gif"></A> <A NAME="tex2html215" HREF="node13.html"><IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="img/up_motif.gif"></A> <A NAME="tex2html209" HREF="node13.html"><IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="img/previous_motif.gif"></A> <A NAME="tex2html217" 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="tex2html219" HREF="node15.html">EXAMPLE 2</A><B> Up:</B> <A NAME="tex2html216" HREF="node13.html">Sample foldings</A><B> Previous:</B> <A NAME="tex2html210" HREF="node13.html">Sample foldings</A><BR><BR><!--End of Navigation Panel--><H2><A NAME="SECTION00081000000000000000"> E<SMALL>XAMPLE 1</SMALL></A></H2><P>The <I>energy dot plot</I> is an integral part of the folding prediction. Consider thefolding of a short RNA sequence: <BR> <TT>ACCCCCUCCU UCCUUGGAUCAAGGGGCUCA A</TT>, <BR>using default parameters. <!-- MATH: $\Delta G= -9.8$ --><IMG WIDTH="83" HEIGHT="29" ALIGN="MIDDLE" BORDER="0" SRC="img7.gif" ALT="$\Delta G= -9.8$">kcal/mole at37<IMG WIDTH="11" HEIGHT="15" ALIGN="BOTTOM" BORDER="0" SRC="img29.gif" ALT="$^{\circ}$">,so <!-- MATH: $\Delta \Delta G= 1.0$ --><IMG WIDTH="84" HEIGHT="15" ALIGN="BOTTOM" BORDER="0" SRC="img121.gif" ALT="$\Delta \Delta G= 1.0$">rather than 5% of <IMG WIDTH="29" HEIGHT="15" ALIGN="BOTTOM" BORDER="0" SRC="img6.gif" ALT="$\Delta G$">.A single,optimal folding is computed. A glance of the <I>energy dot plot</I> , shown in Figure<A HREF="node14.html#EX1P">13</A>, reveals the optimal folding in black dots (symbols), butanother set of yellow dots, indicating base pairs in at least 1 othersuboptimal folding. The default value of `W' (2, from Table<A HREF="#WINDOW">3</A>) is too large for this other folding to be predicted, buta glance at the dot plot shows that something else is there. Whenthe sequence is refolded with `W'=0, a second, totally differentfolding is predicted. Figure <A HREF="node14.html#EX1S">14</A> displays these foldings withindividual bases drawn.<BR><DIV ALIGN="CENTER"><A NAME="EX1P"> </A><A NAME="839"> </A><TABLE WIDTH="50%"><CAPTION><STRONG>Figure 13:</STRONG>The <I> energy dot plot</I> for the ``Example 1''sequence. Surrounding annotation, which would not be legible at thisscale, has been removed. The yellow dots indicate base pairs infoldings within 0.3 kcal/mole of the optimal folding free energy of-9.8 kcal/mole.</CAPTION><TR><TD><IMG WIDTH="354" HEIGHT="350" SRC="img122.gif" ALT="\begin{figure}\centering\epsfig{file=1_zoom.ps}\end{figure}"></TD></TR></TABLE></DIV><BR><P><BR><DIV ALIGN="CENTER"><A NAME="EX1S"> </A><A NAME="842"> </A><TABLE WIDTH="50%"><CAPTION><STRONG>Figure 14:</STRONG>The 2 predicted foldings for the ``Example 1''sequence. (a) The optimal folding with <!-- MATH: $\Delta G= -9.8$ --><IMG WIDTH="83" HEIGHT="29" ALIGN="MIDDLE" BORDER="0" SRC="img7.gif" ALT="$\Delta G= -9.8$">kcal/mole. (b) The suboptimal fold (<!-- MATH: $\Delta G= -9.5$ --><IMG WIDTH="83" HEIGHT="29" ALIGN="MIDDLE" BORDER="0" SRC="img8.gif" ALT="$\Delta G= -9.5$">kcal/mole)found after refolding with `W'=0.</CAPTION><TR><TD><IMG WIDTH="300" HEIGHT="245" SRC="img123.gif" ALT="\begin{figure}\centering\subfigure[]{\epsfig{file=1-again_1_zoom.ps,width=0.3\t......\subfigure[]{\epsfig{file=1-again_2_zoom.ps,width=0.3\textwidth} }\end{figure}"></TD></TR></TABLE></DIV><BR><P><HR><!--Navigation Panel--><A NAME="tex2html218" HREF="node15.html"><IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="img/next_motif.gif"></A> <A NAME="tex2html215" HREF="node13.html"><IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="img/up_motif.gif"></A> <A NAME="tex2html209" HREF="node13.html"><IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="img/previous_motif.gif"></A> <A NAME="tex2html217" 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="tex2html219" HREF="node15.html">EXAMPLE 2</A><B> Up:</B> <A NAME="tex2html216" HREF="node13.html">Sample foldings</A><B> Previous:</B> <A NAME="tex2html210" HREF="node13.html">Sample 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>⌨️ 快捷键说明
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