node11.html

mfold

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 WIDTH="31" HEIGHT="15" ALIGN="BOTTOM" BORDER="0"
 SRC="img27.gif"
 ALT="$\delta \delta G$"></B></TD>
<TD ALIGN="LEFT"><B> Information</B></TD>
</TR>
<TR><TD ALIGN="LEFT">External loop:</TD>
<TD ALIGN="RIGHT">-1.7</TD>
<TD ALIGN="LEFT">4 ss bases &amp;  1 closing helices.</TD>
</TR>
<TR><TD ALIGN="LEFT">Stack:</TD>
<TD ALIGN="RIGHT">-3.4</TD>
<TD ALIGN="LEFT">External closing pair is G<SUP>1</SUP>-C<SUP>72</SUP></TD>
</TR>
<TR><TD ALIGN="LEFT">Stack:</TD>
<TD ALIGN="RIGHT">-2.4</TD>
<TD ALIGN="LEFT">External closing pair is C<SUP>2</SUP>-G<SUP>71</SUP></TD>
</TR>
<TR><TD ALIGN="LEFT">Stack:</TD>
<TD ALIGN="RIGHT">-1.5</TD>
<TD ALIGN="LEFT">External closing pair is G<SUP>3</SUP>-C<SUP>70</SUP></TD>
</TR>
<TR><TD ALIGN="LEFT">Stack:</TD>
<TD ALIGN="RIGHT">-1.3</TD>
<TD ALIGN="LEFT">External closing pair is G<SUP>4</SUP>-U<SUP>69</SUP></TD>
</TR>
<TR><TD ALIGN="LEFT">Stack:</TD>
<TD ALIGN="RIGHT">-1.1</TD>
<TD ALIGN="LEFT">External closing pair is A<SUP>5</SUP>-U<SUP>68</SUP></TD>
</TR>
<TR><TD ALIGN="LEFT"><B> Helix</B></TD>
<TD ALIGN="RIGHT">-9.7</TD>
<TD ALIGN="LEFT">6 base pairs.</TD>
</TR>
<TR><TD ALIGN="LEFT">Multi-loop:</TD>
<TD ALIGN="RIGHT">1.0</TD>
<TD ALIGN="LEFT">External closing pair is U<SUP>6</SUP>-A<SUP>67</SUP></TD>
</TR>
<TR><TD ALIGN="LEFT">&nbsp;</TD>
<TD ALIGN="RIGHT">&nbsp;</TD>
<TD ALIGN="LEFT">10 ss bases &amp;  4 closing helices.</TD>
</TR>
<TR><TD ALIGN="LEFT">Stack:</TD>
<TD ALIGN="RIGHT">-2.1</TD>
<TD ALIGN="LEFT">External closing pair is C<SUP>49</SUP>-G<SUP>65</SUP></TD>
</TR>
<TR><TD ALIGN="LEFT">Stack:</TD>
<TD ALIGN="RIGHT">-2.1</TD>
<TD ALIGN="LEFT">External closing pair is U<SUP>50</SUP>-A<SUP>64</SUP></TD>
</TR>
<TR><TD ALIGN="LEFT">Stack:</TD>
<TD ALIGN="RIGHT">-2.2</TD>
<TD ALIGN="LEFT">External closing pair is G<SUP>51</SUP>-C<SUP>63</SUP></TD>
</TR>
<TR><TD ALIGN="LEFT">Stack:</TD>
<TD ALIGN="RIGHT">-2.1</TD>
<TD ALIGN="LEFT">External closing pair is U<SUP>52</SUP>-A<SUP>62</SUP></TD>
</TR>
<TR><TD ALIGN="LEFT"><B> Helix</B></TD>
<TD ALIGN="RIGHT">-8.5</TD>
<TD ALIGN="LEFT">5 base pairs.</TD>
</TR>
<TR><TD ALIGN="LEFT">Hairpin loop:</TD>
<TD ALIGN="RIGHT">4.8</TD>
<TD ALIGN="LEFT">Closing pair is G<SUP>53</SUP>-C<SUP>61</SUP></TD>
</TR>
<TR><TD ALIGN="LEFT">Stack:</TD>
<TD ALIGN="RIGHT">-3.3</TD>
<TD ALIGN="LEFT">External closing pair is C<SUP>27</SUP>-G<SUP>43</SUP></TD>
</TR>
<TR><TD ALIGN="LEFT">Stack:</TD>
<TD ALIGN="RIGHT">-2.1</TD>
<TD ALIGN="LEFT">External closing pair is C<SUP>28</SUP>-G<SUP>42</SUP></TD>
</TR>
<TR><TD ALIGN="LEFT">Stack:</TD>
<TD ALIGN="RIGHT">-2.1</TD>
<TD ALIGN="LEFT">External closing pair is A<SUP>29</SUP>-U<SUP>41</SUP></TD>
</TR>
<TR><TD ALIGN="LEFT">Stack:</TD>
<TD ALIGN="RIGHT">-2.4</TD>
<TD ALIGN="LEFT">External closing pair is G<SUP>30</SUP>-C<SUP>40</SUP></TD>
</TR>
<TR><TD ALIGN="LEFT"><B> Helix</B></TD>
<TD ALIGN="RIGHT">-9.9</TD>
<TD ALIGN="LEFT">5 base pairs.</TD>
</TR>
<TR><TD ALIGN="LEFT">Hairpin loop:</TD>
<TD ALIGN="RIGHT">5.7</TD>
<TD ALIGN="LEFT">Closing pair is A<SUP>31</SUP>-U<SUP>39</SUP></TD>
</TR>
<TR><TD ALIGN="LEFT">Stack:</TD>
<TD ALIGN="RIGHT">-3.4</TD>
<TD ALIGN="LEFT">External closing pair is G<SUP>10</SUP>-C<SUP>25</SUP></TD>
</TR>
<TR><TD ALIGN="LEFT">Stack:</TD>
<TD ALIGN="RIGHT">-2.1</TD>
<TD ALIGN="LEFT">External closing pair is C<SUP>11</SUP>-G<SUP>24</SUP></TD>
</TR>
<TR><TD ALIGN="LEFT">Stack:</TD>
<TD ALIGN="RIGHT">-2.4</TD>
<TD ALIGN="LEFT">External closing pair is U<SUP>12</SUP>-A<SUP>23</SUP></TD>
</TR>
<TR><TD ALIGN="LEFT"><B> Helix</B></TD>
<TD ALIGN="RIGHT">-7.9</TD>
<TD ALIGN="LEFT">4 base pairs.</TD>
</TR>
<TR><TD ALIGN="LEFT">Hairpin loop:</TD>
<TD ALIGN="RIGHT">3.9</TD>
<TD ALIGN="LEFT">Closing pair is C<SUP>13</SUP>-G<SUP>22</SUP></TD>
</TR>
</TABLE></TD></TR>
</TABLE>
</DIV>
<BR>
<P>
 <SMALL>`FILE_NAME.SS-COUNT' :  </SMALL> If <I>l</I> foldings are predicted, then <I>ss-count(i)</I>
is the number of times that <I>r</I><SUB><I>i</I></SUB> is single
stranded in these foldings. Thus 
<I>ss-count(i)/l</I>
is a <I>sample based probability</I> for single strandedness. The ss-count file contains
the number of computed foldings in the first record.  The <I>i</I><SUP><I>th</I></SUP>subsequent record contains <I>i</I> and <I>ss-count(i)</I>.
This file may be
used to predict which regions of an RNA are likely to be single
stranded, and values of ss-count, averaged over a window of perhaps
5 to 25 base pairs, are often plotted.  This file is also used for
annotating plotted structures.

<P>
 <SMALL>`FILE_NAME_<I>I</I>.PLT2' :  </SMALL> This is an intermediate, device
independent plot file. It is the output of <I>mfold</I>'s adaptation of
the <I>naview</I> program for plotting secondary structures. This file
is used as input to the <I>plt22ps</I> and <I>plt22gif</I> programs. It
was originally intended to be used as input to the <I>plt2</I> plotting
package [<A
 HREF="node19.html#BEAR8101">39</A>], but this software is now old and not maintained.

<P>
 <SMALL>`FILE_NAME_<I>I</I>.PS' :  </SMALL> This is a PostScript file of a
secondary structure. It is the output of the <I>plt22ps</I> program.

<P>
 <SMALL>`FILE_NAME_<I>I</I>.GIF' :  </SMALL> This is an image file (gif) of a
secondary structure. It is the output of the <I>plt22gif</I> program.

<P>
The progression from ct file to images of secondary structures is: <BR>
`file_name_i.ct' 
<!-- MATH: $\rightarrow$ -->
<IMG
 WIDTH="19" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
 SRC="img120.gif"
 ALT="$\rightarrow$">
<I>naview</I> 
<!-- MATH: $\rightarrow$ -->
<IMG
 WIDTH="19" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
 SRC="img120.gif"
 ALT="$\rightarrow$">`file_name_i.plt2' 
<!-- MATH: $\rightarrow$ -->
<IMG
 WIDTH="19" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
 SRC="img120.gif"
 ALT="$\rightarrow$">
<I>plt22ps</I> 
<!-- MATH: $\rightarrow$ -->
<IMG
 WIDTH="19" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
 SRC="img120.gif"
 ALT="$\rightarrow$">`file_name_i.ps' <BR>
or  <BR>
`file_name_i.ct' 
<!-- MATH: $\rightarrow$ -->
<IMG
 WIDTH="19" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
 SRC="img120.gif"
 ALT="$\rightarrow$">
naview 
<!-- MATH: $\rightarrow$ -->
<IMG
 WIDTH="19" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
 SRC="img120.gif"
 ALT="$\rightarrow$">`file_name_i.plt2' 
<!-- MATH: $\rightarrow$ -->
<IMG
 WIDTH="19" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
 SRC="img120.gif"
 ALT="$\rightarrow$">
<I>plt22gif</I> 
<!-- MATH: $\rightarrow$ -->
<IMG
 WIDTH="19" HEIGHT="14" ALIGN="BOTTOM" BORDER="0"
 SRC="img120.gif"
 ALT="$\rightarrow$">`file_name_i.gif'

<P>
 <SMALL>`FILE_NAME.HTML' :  </SMALL> This is a simple html file that links
together some of the output files. It is an early version of a format
originally used by the <I>mfold</I> web server.

<P>
 <SMALL>`FILE_NAME.LOG' :  </SMALL> This is a log file containing the standard
output and standard error of the various programs and scripts that
make up <I>mfold</I> . It can be useful for debugging.

<P>
 <SMALL>`FILE_NAME.PNT' :  </SMALL> This is a human readable file containing
the entire input sequence. Every 10<SUP><I>th</I></SUP> base is labeled. In
addition, auxiliary information is incorporated, if there is any. 
Bases that are forced to be double stranded have the
letter `F' underneath. Those that are forced to be single stranded have the
letter `P' underneath. Pairs of rounded brackets `(` and `)'
underline forced base pairs, and pairs of curly brackets `{` and
`}' underline prohibited base pairs. If 2 disjoint segments are
prohibited from pairing with one another, then these segments are
highlighted by underlining the residues of the first with a common
lowercase letter, and the residues of the second with the same letter
in uppercase. Different letters are used for different prohibited
pairs. `F' and `P' are not used in this case.

<P>
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<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>
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