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<TITLE></TITLE><HEAD><TITLE>mfold Documentation</TITLE></HEAD><BODY BGCOLOR=#ffccaa TEXT=#000000 LINK=#005030 VLINK=#305050>Michael Zuker, Rensselaer Polytechnic Institute<HR><DL><A NAME=ION><DT> <IMG SRC="l_yellow.gif" HSPACE=10><FONT SIZE=5><I>Ionic Conditions </I></FONT></A><DD> The corrections for [Na<SUP>+</SUP>] and[Mg<SUP>++</SUP>] have been empirically derived. They arecurrently being used only for DNA folding, where the conditions underwhich free energy measurements were made, [Na<SUP>+</SUP>] = 1 Mand [Mg<SUP>++</SUP>] = 0 M, are far from reasonablephysiological conditions. <OL><LI> <U>Oligomer correction:</U> [Na<SUP>+</SUP>] should bekept between 0.01 M and 1 M, and [Mg<SUP>++</SUP>] should be no largerthan 0.1 M. This correction is most likely valid for foldings thatresult in stems of up to 20 base pairs, including bulges and interiorloops. It is certainly not valid for a long stretch of perfectWatson-Crick base pairs.<LI> <U>Polymer correction:</U> [Mg<SUP>++</SUP>] must be0. The combined effect of [Na<SUP>+</SUP>] and [Mg<SUP>++</SUP>] inpolymers is still not understood. This correction should be used whenlong stems form. A "long stem" contains about 20 or more consecutivenucleotides that are base paired or in bulge/interior loops .</OL><HR SIZE=2 NOSHADE> <P><A NAME=PERCENT><DT> <IMG SRC="l_green.gif" HSPACE=10><FONT SIZE=5><I>Percent suboptimality</I></FONT></A><DD> If this number is set to <I>p</I>, then only foldings within<I>p%</I> from the minimum free energy will be computed. The <I>energydot plot</I> contains the superposition of all possible foldingswithin <I>p%</I> of the minimum energy. An energy increment of <B>lessthan</B> 1 kcal/mole is rounded up to 1 kcal/mole. Similarly, anincrement of more than 12.0 kcal/mole is rounded down to 12.0kcal/mole.<HR SIZE=2 NOSHADE> <P><A NAME=EDP><DT> <IMG SRC="l_cyan.gif" HSPACE=10><FONT SIZE=5><I>Energy dot plot</I></FONT></A><DD> In the upper triangular region, a dot in row <I>i</I> and column<I>j</I> represents a base pair between the <I>i<SUP>th</SUP></I> and<I>j<SUP>th</SUP></I> bases. The black dots represent all the optimalfoldings. The colored, smaller dots represent the superposition of allpossible suboptimal foldings within <I>p%</I> of the minimum freeenergy, where <I>p</I> is the maximium percent deviation from theminimum free energy. The color ranges are red, blue and yellow;representing base pairs that are in foldings within <I>p/3%</I>,<I>2p/3%</I> and <I>p%</I> of the minimum free energy,respectively. Thus the yellow dots represent base pairs that are leastlikely to form.<HR SIZE=2 NOSHADE> <P><A NAME=MAX_FOLDS><DT> <IMG SRC="l_purple.gif" HSPACE=10><FONT SIZE=5><I>Maximium number of foldings</I></FONT></A><DD> The <I>upper bound</I> on the number of foldings that arecomputed is not necessary. The folding algorithm automaticallycomputes a selection of secondary structures within the prescribedenergy increment and stops when no more <I>sufficiently different</I>foldings can be found. See also the definition of the <I>window</I>parameter <A HREF="#WINDOW">(below)</A>.<HR SIZE=2 NOSHADE> <P><A NAME=GIFRES><DT> <IMG SRC="l_blue.gif" HSPACE=10><FONT SIZE=5><I>Image resolution - png & jpg files</I></FONT></A><DD> The default value of 72 pixels per inch (Regular) gives images thatare very good for relatively short sequences. Longer sequences withcomplicated folds require higher resolution. The resolution optionnow computes images faster than before using custom softwarethat in turn uses Bradley Sherman's <B>tgd</B> package which itself isbased on Tom Boutell's <B>gd</B> library. <HR SIZE=2 NOSHADE> <P><A NAME=MODE><DT> <IMG SRC="l_red.gif" HSPACE=10><FONT SIZE=5><I>Structure format</I></FONT></A><DD> The PostScript, png & jpg plots of secondary structure have 2 formats.In the first format, individual bases are shown and base pairs aredepicted by colored dots. This is the "Bases" option. Otherwise, onlyan outline of the secondary structure is drawn, and base pairs becomecolored line segments. This is the "Outline" option. The default"Automatic" option draws bases when sequence length is less than 800,and an outline otherwise.<HR SIZE=2 NOSHADE> <P><A NAME=LAB_FR><DT> <IMG SRC="l_grey.gif" HSPACE=10><FONT SIZE=5><I>Structure numbering frequency</I></FONT></A><DD> Individual structures are numbered, starting at some number<B>N</B>, and continuing with every multiple of <B>N</B>. When<B>N</B>=0, there is no structure numbering. If the user does notchoose a value, it will be taken from the table below. <P><CENTER><TABLE BORDER=3 CELLSPACING=3 CELLPADDING=3><CAPTION ALIGN=BOTTOM><I>Default numbering increment for structures.</I></CAPTION><TR><TH ALIGN=CENTER BGCOLOR="#808000">Sequence length </TD> <TH ALIGN=CENTER BGCOLOR="#008080">Numbering increment</TD></TR><TR><TD ALIGN=CENTER> 1-50 </TD><TD ALIGN=CENTER> 10 </TD></TR><TR><TD ALIGN=CENTER> 51-300 </TD><TD ALIGN=CENTER> 20 </TD></TR><TR><TD ALIGN=CENTER> > 300 </TD><TD ALIGN=CENTER> 50 </TD></TR></TABLE></CENTER><HR SIZE=2 NOSHADE> <P><A NAME=ROT_ANG><DT> <IMG SRC="l_brown.gif" HSPACE=10><FONT SIZE=5><I>Structure rotation</I></FONT></A><DD> Plotted structures may be rotated through a user selected angle (in degrees). The default value is 0, and entries between ⌨️ 快捷键说明
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