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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>Optimal and suboptimal foldings</TITLE><META NAME="description" CONTENT="Optimal and suboptimal foldings"><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="node10.html"><LINK REL="up" HREF="node9.html"><LINK REL="next" HREF="node12.html"></HEAD><BODY BGCOLOR=#FFDEAD TEXT=#202020 LINK=#800000 ALINK=#ffff00 VLINK=#353976><!--Navigation Panel--><A NAME="tex2html184" HREF="node12.html"><IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="img/next_motif.gif"></A> <A NAME="tex2html181" HREF="node9.html"><IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="img/up_motif.gif"></A> <A NAME="tex2html177" HREF="node10.html"><IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="img/previous_motif.gif"></A> <A NAME="tex2html183" 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="tex2html185" HREF="node12.html">AUXILIARY AND INDIVIDUAL PROGRAMS</A><B> Up:</B> <A NAME="tex2html182" HREF="node9.html">OUTPUT</A><B> Previous:</B> <A NAME="tex2html178" HREF="node10.html">The energy dot plot</A><BR><BR><!--End of Navigation Panel--><H3><A NAME="SECTION00072200000000000000"><I>Optimal and suboptimal foldings</I></A></H3><P><I>Mfold</I> predicts a number of optimal and suboptimal foldings. They areautomatically predicted in order of increasing free energy, althoughthis order may change when the more exact <I>efn2</I> program is usedto re-evaluate free energies. The number of computed foldings islimited directly by the MAX parameter, and in more subtle ways by theP and W parameters. It should be stated clearly here that while the<I>energy dot plot</I> rigorously displays all possible base pairs that can take part inall possible foldings within <!-- MATH: $\Delta \Delta G$ --><IMG WIDTH="42" HEIGHT="15" ALIGN="BOTTOM" BORDER="0" SRC="img9.gif" ALT="$\Delta \Delta G$">of <IMG WIDTH="29" HEIGHT="15" ALIGN="BOTTOM" BORDER="0" SRC="img6.gif" ALT="$\Delta G$">,the computation offoldings is arbitrary. They do not represent a statistical sample oflikely foldings, but rather a collection of foldings that show thevariation that is possible within optimal and suboptimal foldings. <P>The collection of triples, <!-- MATH: $i,j,\Delta G(i,j)$ --><IMG WIDTH="88" HEIGHT="31" ALIGN="MIDDLE" BORDER="0" SRC="img115.gif" ALT="$i,j,\Delta G(i,j)$">,for all possible base pairsis sorted in order of increasing <!-- MATH: $\Delta G(i,j)$ --><IMG WIDTH="62" HEIGHT="31" ALIGN="MIDDLE" BORDER="0" SRC="img101.gif" ALT="$\Delta G(i,j)$">.The algorithm toconstruct foldings proceeds as follows:<DL COMPACT><DT>1.<DD>The base pair at the top of the list is selected, and an optimalfolding <I>containing the selected base pair</I> is computed.<DT>2.<DD>All base pairs in the computed folding, as well as all thosewithin a distance of W of base pairs in the computed folding, arecrossed off the list.<DT>3.<DD>The computed folding is retained if it contains at least W basepairs that were not found in previous foldings.</DL>The first structure is always retained, even if itcontains fewer than W base pairs. Steps 1 to 3 are repeated untileither MAX structures have been computed and retained, or until thereare no more base pairs on the list.<P><I>Mfold</I> creates a number of files associated with predicted structures.The files marked with an optional ``html'' are created only whenRUN_TYPE is html. Files that contain an underscore, `_', in theirnames enumerate the individual foldings, so that `file_name_<I>i</I>.ct'refers to the ct file for the <I>i</I><SUP><I>th</I></SUP> predicted structure.<P> <SMALL>`FILE_NAME.OUT(.HTML)' : </SMALL> This is a text file (html file)containing a plain text form of output for each of the predictedfoldings. It is useful because it can always be displayed and isintelligible for foldings on short sequences. The selected base pairsfor computing each structure are specially marked with a <code>`|'</code> aboveand a <code>`^'</code> below. A sample output is shown in Figure <A HREF="node11.html#OUT">11</A>.<P><BR><DIV ALIGN="CENTER"><A NAME="OUT"> </A><A NAME="834"> </A><TABLE WIDTH="100%"><CAPTION><STRONG>Figure 11:</STRONG>The second and final folding of <I> S. cerevisiae</I>Phe-tRNA at 37°,with P=5% and W=3 (default values). (a) Theselected base pair is G<SUP>51</SUP>-C<SUP>63</SUP>. The base numbers are placedso that the least significant digit, always a 0, is above orbelow the enumerated base. (b) The usual plotted representation. The<I> efn2</I> program has adjusted <IMG WIDTH="29" HEIGHT="15" ALIGN="BOTTOM" BORDER="0" SRC="img6.gif" ALT="$\Delta G$">from -22.3 to -22.7 kcal/mole</CAPTION><TR><TD><PRE> FOLDING BASES 1 TO 76 OF tRNA Initial ENERGY = -22.3 10 ---- UUA AGU GCGGAU GCUC U CGCUUA CGAG GACCA --A AGG 70 20 30 G CUG CCAGA GGUCU A - AGA 40 50 AGGUC | UUC CUGUG GACAC G ----- ^ CUA 60 </PRE></TD><TD><IMG SRC="tRNA_1_zoom.gif" BORDER="0"></TD></TR><TR><TH> (a) Text </TH><TH>(b) Plot</TH></TR></TABLE></DIV><BR><P> <SMALL>`FILE_NAME_<I>I</I>.CT' : </SMALL> The ``ct'' file (<U>c</U>onnect<U>t</U>able) contains the sequence and base pair information,and is meant to be an input file for a structure drawing program. Inaddition to containing base pair information, it also lists the 5'and 3' neighbor of each base, allowing for the representation ofcircular RNA or multiple molecules. The ct file also lists thehistorical base numbering in the original sequence, as bases and basepairs are numbered according from 1 to the size of the foldedsegment. A portion of a ct file is displayed in Figure <A HREF="node11.html#CT">12</A>.<BR><DIV ALIGN="CENTER"><A NAME="CT"> </A><A NAME="835"> </A><TABLE BORDER=5 CELLPADDING=10><CAPTION><STRONG>Figure 12:</STRONG>The ct file for the second and final folding of <I>S. cerevisiae</I> Phe-tRNA at 37°,with default parameters.The first record displays the fragment size (76), <IMG WIDTH="29" HEIGHT="15" ALIGN="BOTTOM" BORDER="0" SRC="img6.gif" ALT="$\Delta G$">and sequencename. The <I>i</I><SUP><I>th</I></SUP> subsequent record contains, in order, <I>i</I>,<I>r</I><SUB><I>i</I></SUB>, the index of the 5'-connecting base, the index of the3'-connecting base, the index of the paired base and the historicalnumbering of the <I>i</I><SUP><I>th</I></SUP> base in the original sequence. The 5',3' and base pair indices are 0 when there is no connection or basepair.</CAPTION><TR><TD BGCOLOR=#CCCC80><PRE> 76 ENERGY = -24.4 [initially -23.2] yeast tRNA Phe 1 G 0 2 72 1 2 C 1 3 71 2 3 G 2 4 70 3 4 G 3 5 69 4 5 A 4 6 68 5 6 U 5 7 67 6 7 U 6 8 0 7 8 U 7 9 0 8 ... 67 A 66 68 6 67 68 U 67 69 5 68 69 U 68 70 4 69 70 C 69 71 3 70 71 G 70 72 2 71 72 C 71 73 1 72 73 A 72 74 0 73 74 C 73 75 0 74 75 C 74 76 0 75 76 A 75 0 0 76</PRE></TD></TR></TABLE></DIV><BR><P> <SMALL>`FILE_NAME.DET(.HTML)' : </SMALL> This is a text file (html file)containing the <U>det</U>ailed breakdown of each folding intoloops, and the corresponding decomposition of the overall free energy,<IMG WIDTH="29" HEIGHT="15" ALIGN="BOTTOM" BORDER="0" SRC="img6.gif" ALT="$\Delta G$">,into the free energy contributions, <!-- MATH: $\delta \delta G$ --><IMG WIDTH="31" HEIGHT="15" ALIGN="BOTTOM" BORDER="0" SRC="img27.gif" ALT="$\delta \delta G$">,for each loop.A sample output is shown in Table <A HREF="#DET">4</A>.<BR><DIV ALIGN="CENTER"><A NAME="836"> </A><TABLE><CAPTION><STRONG>Table 4:</STRONG>Free energy details for the second and finalfolding of <I> S. cerevisiae</I> Phe-tRNA at 37°,with defaultfolding parameters. This layout mimics the html output.</CAPTION><TR><TD>Loop Free-Energy Decomposition <BR>Structure 3 <BR>tRNA.seq Initial Free energy = -22.3 <BR> <TABLE CELLPADDING=3 BORDER="1"><TR><TD ALIGN="LEFT"><B> Structural element</B></TD><TD ALIGN="RIGHT"><B> <!-- MATH: $\delta \delta G$ -->⌨️ 快捷键说明
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