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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>Constrained folding</TITLE><META NAME="description" CONTENT="Constrained folding"><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="node7.html"><LINK REL="previous" HREF="node5.html"><LINK REL="up" HREF="FEBS98-html.html"><LINK REL="next" HREF="node7.html"></HEAD><BODY BGCOLOR=#FFDEAD TEXT=#202020 LINK=#800000 ALINK=#ffff00 VLINK=#353976><!--Navigation Panel--><A NAME="tex2html124" HREF="node7.html"><IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="img/next_motif.gif"></A> <A NAME="tex2html121" HREF="FEBS98-html.html"><IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="img/up_motif.gif"></A> <A NAME="tex2html115" HREF="node5.html"><IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="img/previous_motif.gif"></A> <A NAME="tex2html123" 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="tex2html125" HREF="node7.html">Running the programs</A><B> Up:</B> <A NAME="tex2html122" HREF="FEBS98-html.html">Algorithms and Thermodynamics for</A><B> Previous:</B> <A NAME="tex2html116" HREF="node5.html">Loops and Nearest neighbor</A><BR><BR><!--End of Navigation Panel--><H1><A NAME="SECTION00060000000000000000">Constrained folding</A></H1><P>In addition to the free energy rules, specific constraints may be usedto force or prohibit base pairs. A special file containing commands toconstrain folding is used. The command syntax is rigid. The variouscommands and syntax are given below.<P><DL COMPACT><DT>1.<DD>Forcing a string of consecutive bases to pair. <BR>Syntax: <I>F i 0 k</I> <BR>Ribonucleotides <!-- MATH: $r_{i},r_{i+1}, \dots, r_{i+k-1}$ --><IMG WIDTH="132" HEIGHT="28" ALIGN="MIDDLE" BORDER="0" SRC="img86.gif" ALT="$r_{i},r_{i+1}, \dots, r_{i+k-1}$">are forced to bedouble stranded. The partners for these bases are chosen by the program.As an example, the command: <BR><I>F 23 0 5</I> <BR>would cause bases 23, 24, 25, 26 and 27 to pair. <P><DT>2.<DD>Forcing a string of consecutive base pairs. <BR>Syntax: <I>F i j k</I> <BR>Base pairs <!-- MATH: $r_{i}-r_{j}, r_{i+1}-r_{j-1}, r_{i+2}-r_{j-2}, \dots,r_{i+k-1}.r_{j-k+1}$ --><IMG WIDTH="352" HEIGHT="28" ALIGN="MIDDLE" BORDER="0" SRC="img87.gif" ALT="$r_{i}-r_{j}, r_{i+1}-r_{j-1}, r_{i+2}-r_{j-2}, \dots,r_{i+k-1}.r_{j-k+1}$">are forced to occur.This is the same thing as forcing a helix to form. The helix isdesignated by its (external) closing base pair, <I>i</I>.<I>j</I>.As an example, the command: <BR><I>F 2 110 3</I> <BR>would force base pairs 2.110, 3.109 and 4.108. Note that thesebase pairs <B>must be able to form!</B> Be aware also that <I>mfold</I> filters out isolated base pairs. <P><DT>3.<DD>Prohibiting a string of consecutive bases from pairing. <BR>Syntax: <I>P i 0 k</I> <BR>Ribonucleotides <!-- MATH: $r_{i},r_{i+1}, \dots, r_{i+k-1}$ --><IMG WIDTH="132" HEIGHT="28" ALIGN="MIDDLE" BORDER="0" SRC="img86.gif" ALT="$r_{i},r_{i+1}, \dots, r_{i+k-1}$">are prevented frompairing. <P><DT>4.<DD>Prohibiting a string of consecutive base pairs <BR>Syntax: <I>P i j k</I> <BR>Base pairs <!-- MATH: $r_{i}-r_{j}, r_{i+1}-r_{j-1}, r_{i+2}-r_{j-2}, \dots,r_{i+k-1}.r_{j-k+1}$ --><IMG WIDTH="352" HEIGHT="28" ALIGN="MIDDLE" BORDER="0" SRC="img87.gif" ALT="$r_{i}-r_{j}, r_{i+1}-r_{j-1}, r_{i+2}-r_{j-2}, \dots,r_{i+k-1}.r_{j-k+1}$">are not allowed to form. This is equivalent toprohibiting a helix.<DT>5.<DD>Prohibiting 1 segment of a sequence from pairing with another <BR>Syntax: <I>P i-j k-l</I> <BR>where <IMG WIDTH="37" HEIGHT="28" ALIGN="MIDDLE" BORDER="0" SRC="img88.gif" ALT="$i \leq j$">and <IMG WIDTH="38" HEIGHT="29" ALIGN="MIDDLE" BORDER="0" SRC="img89.gif" ALT="$k \leq l$">.In this case,no base pairs are allowed between <!-- MATH: $r_{i}, r_{i+1}, \dots, r_{j}$ --><IMG WIDTH="101" HEIGHT="28" ALIGN="MIDDLE" BORDER="0" SRC="img90.gif" ALT="$r_{i}, r_{i+1}, \dots, r_{j}$">and<!-- MATH: $r_{k}, r_{k+1}, \dots, r_{l}$ --><IMG WIDTH="104" HEIGHT="28" ALIGN="MIDDLE" BORDER="0" SRC="img91.gif" ALT="$r_{k}, r_{k+1}, \dots, r_{l}$">.Note that the 2 segments need not bedistinct. For example, the command: <BR><I>P i-j i-j</I> <BR>will not allow <!-- MATH: $r_{i}, r_{i+1}, \dots, r_{j}$ --><IMG WIDTH="101" HEIGHT="28" ALIGN="MIDDLE" BORDER="0" SRC="img90.gif" ALT="$r_{i}, r_{i+1}, \dots, r_{j}$">to pair with itself.<DT>6.<DD>Annotated bases. <BR><DL COMPACT><DT>(a)<DD><I>mfold</I> recognizes A, C, G, U and T. In RNA folding, a `T' will betreated as a `U'; and <I>vice versa</I> for DNA folding. In addition,B, D, H and V are recognized as A, C, G and U/T, respectively. Bases marked in this way are regarded as susceptible to nucleasecleavage. They are allowed to pair only if their 3' neighbor isunpaired. This is an old feature of <I>mfold</I> . <DT>(b)<DD><I>mfold</I> also recognizes W, X, Y and Z as A, C, G and U/T,respectively. These bases are regarded as ``modified'' and are allowedto pair only at the ends of helices. At this time, thecommonly used ambiguous codes shown in Table <A HREF="#AMBIG">2</A> are notsupported by <I>mfold</I> .<BR><DIV ALIGN="CENTER"><A NAME="824"> </A><TABLE><CAPTION><STRONG>Table 2:</STRONG>Unsupported ambiguous codes for RNA/DNA. <I> mfold</I> does not currently support the convention for ambiguouscodes. Unrecognized bases will not be allowed to pair.</CAPTION><TR><TD><TABLE CELLPADDING=3 BORDER="1"><TR><TD ALIGN="LEFT"><B> Ambiguity</B></TD><TD ALIGN="CENTER">A,G</TD><TD ALIGN="CENTER">C,U/T</TD><TD ALIGN="CENTER">A,U/T</TD><TD ALIGN="CENTER">C,G</TD><TD ALIGN="CENTER">A,C</TD><TD ALIGN="CENTER">G,U/T</TD></TR><TR><TD ALIGN="LEFT"><B> Code letter</B></TD><TD ALIGN="CENTER">R</TD><TD ALIGN="CENTER">Y</TD><TD ALIGN="CENTER">W</TD><TD ALIGN="CENTER">S</TD><TD ALIGN="CENTER">M</TD><TD ALIGN="CENTER">K</TD></TR><TR><TD ALIGN="LEFT"><B> Ambiguity</B></TD><TD ALIGN="CENTER">C,G,U/T</TD><TD ALIGN="CENTER">A,G,U/T</TD><TD ALIGN="CENTER">A,C,U/T</TD><TD ALIGN="CENTER">A,C,G</TD><TD ALIGN="CENTER">A,C,G,U/T</TD><TD ALIGN="CENTER"> </TD></TR><TR><TD ALIGN="LEFT"><B> Code letter</B></TD><TD ALIGN="CENTER">B</TD><TD ALIGN="CENTER">D</TD><TD ALIGN="CENTER">H</TD><TD ALIGN="CENTER">V</TD><TD ALIGN="CENTER">N</TD><TD ALIGN="CENTER"> </TD></TR></TABLE></TD></TR></TABLE></DIV><BR></DL></DL><P><HR><!--Navigation Panel--><A NAME="tex2html124" HREF="node7.html"><IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="img/next_motif.gif"></A> <A NAME="tex2html121" HREF="FEBS98-html.html"><IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="img/up_motif.gif"></A> <A NAME="tex2html115" HREF="node5.html"><IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="img/previous_motif.gif"></A> <A NAME="tex2html123" 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="tex2html125" HREF="node7.html">Running the programs</A><B> Up:</B> <A NAME="tex2html122" HREF="FEBS98-html.html">Algorithms and Thermodynamics for</A><B> Previous:</B> <A NAME="tex2html116" HREF="node5.html">Loops and Nearest neighbor</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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