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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>COMMAND LINE PARAMETERS</TITLE><META NAME="description" CONTENT="COMMAND LINE PARAMETERS"><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="node9.html"><LINK REL="previous" HREF="node7.html"><LINK REL="up" HREF="node7.html"><LINK REL="next" HREF="node9.html"></HEAD><BODY BGCOLOR=#FFDEAD TEXT=#202020 LINK=#800000 ALINK=#ffff00 VLINK=#353976><!--Navigation Panel--><A NAME="tex2html151" HREF="node9.html"><IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="img/next_motif.gif"></A> <A NAME="tex2html148" HREF="node7.html"><IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="img/up_motif.gif"></A> <A NAME="tex2html142" HREF="node7.html"><IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="img/previous_motif.gif"></A> <A NAME="tex2html150" 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="tex2html152" HREF="node9.html">OUTPUT</A><B> Up:</B> <A NAME="tex2html149" HREF="node7.html">Running the programs</A><B> Previous:</B> <A NAME="tex2html143" HREF="node7.html">Running the programs</A><BR><BR><!--End of Navigation Panel--><H2><A NAME="SECTION00071000000000000000"> <SMALL>COMMAND LINE PARAMETERS</SMALL></A></H2><P>These command line parameters can only be fully understood when themeaning of the different type of output files, described in the nextsubsection, is known.<P>SEQ :   The user must supply the name of a sequence file,called `file_name' here. If `file_name' ends with a suffix, that is, aperiod (`.') followed by other characters, then the suffix is removedand the result is called `fold_name'. If no periods exist in`file_name', then `fold_name' = `file_name'. For example, if thesequence is stored in `trna.seq', then `file_name' becomes `trna'. If,on the other hand, the sequence file is named `trna-file', then`file_name' becomes `trna-file'. The `file_name', which may containperiods, becomes the `prefix' for all the output files, such as`file_name.out', `file_name.det' and others.<P>Accepted sequence file formats are <I>GenBank</I>, <I>EMBL</I>, <I>FASTA</I> and <I>IntelliGenetics</I>. The sequence file may containmultiple sequences. At present, the <I>mfold</I> script will fold thefirst sequence by default. A new command line variable, NUM=`#' may beadded that directs the script to fold the `#'<SUP><I>th</I></SUP> sequence in theinput file.<P>AUX :   This is the name of an auxiliary input file of foldingconstraints. If this parameter is not used, <I>mfold</I> looks for a filenamed `fold_name.aux'. If this file exists and is not empty, then itis interpreted as a constraint file. Thus constraints may be usedwithout the use of this command line parameter.<P>RUN_TYPE :   This parameter takes on 2 values; `text', bydefault, and `html' otherwise. The text option creates plain textfiles for the `fold_name.out' and `fold_name.det' files describedbelow. The html option creates HTML versions of these files fordisplay with a web browser.<P>NA :   This parameter takes on 2 values; `RNA' by default, and`DNA' otherwise. It tells <I>mfold</I> what type of nucleic acid is being folded.<P>LC :   This parameter takes on 2 values; `linear' by default,and `circular' otherwise. It indicates to <I>mfold</I> whether a linear orcircular nucleic acid is being folded.<P>T :   This is the temperature, in &#176;C. By default, itis 37&#176;C.Non-integral values will be rounded down to thenearest integer. Values should be in the range <!-- MATH: $0 \leq T \leq 100$ --><IMG WIDTH="89" HEIGHT="29" ALIGN="MIDDLE" BORDER="0" SRC="img92.gif" ALT="$0 \leq T \leq 100$">.<P>P :   This is the percent suboptimality for computing the <I>energy dot plot</I> and suboptimal foldings. The default value is5%. This parameter controls the value of the free energy increment,<!-- MATH: $\Delta \Delta G$ --><IMG WIDTH="42" HEIGHT="15" ALIGN="BOTTOM" BORDER="0" SRC="img9.gif" ALT="$\Delta \Delta G$">.<!-- MATH: $\Delta \Delta G$ --><IMG WIDTH="42" HEIGHT="15" ALIGN="BOTTOM" BORDER="0" SRC="img9.gif" ALT="$\Delta \Delta G$">is set to P% of <IMG WIDTH="29" HEIGHT="15" ALIGN="BOTTOM" BORDER="0" SRC="img6.gif" ALT="$\Delta G$">,thecomputed minimum free energy. The <I>energy dot plot</I> shows onlythose base pairs that are in foldings with free energy  <!-- MATH: $\leq \Delta G+ \Delta \Delta G$ --><IMG WIDTH="104" HEIGHT="29" ALIGN="MIDDLE" BORDER="0" SRC="img93.gif" ALT="$\leq \Delta G+ \Delta \Delta G$">.Similarly, the free energies of computed foldingsare in the range from <IMG WIDTH="29" HEIGHT="15" ALIGN="BOTTOM" BORDER="0" SRC="img6.gif" ALT="$\Delta G$">to <!-- MATH: $\Delta G+ \Delta \Delta G$ --><IMG WIDTH="88" HEIGHT="29" ALIGN="MIDDLE" BORDER="0" SRC="img94.gif" ALT="$\Delta G+ \Delta \Delta G$">.Nomatter the value of P, <I>mfold</I> currently keeps <!-- MATH: $\Delta \Delta G$ --><IMG WIDTH="42" HEIGHT="15" ALIGN="BOTTOM" BORDER="0" SRC="img9.gif" ALT="$\Delta \Delta G$">in therange <!-- MATH: $1 \leq \Delta \Delta G\leq 12$ --><IMG WIDTH="109" HEIGHT="29" ALIGN="MIDDLE" BORDER="0" SRC="img95.gif" ALT="$1 \leq \Delta \Delta G\leq 12$">(kcal/mole).<P>W :   This is the window parameter that controls the number offoldings that are automatically computed by <I>mfold</I> . `W' may be thoughtof as a distance parameter. The distance between 2 base pairs, <I>i</I>.<I>j</I>and <I>i</I>'.<I>j</I>' may be defined as <!-- MATH: $\max\{|i-i'|,|j-j'|\}$ --><IMG WIDTH="147" HEIGHT="31" ALIGN="MIDDLE" BORDER="0" SRC="img96.gif" ALT="$\max\{\vert i-i'\vert,\vert j-j'\vert\}$">.Then if <I>k</I>-1 foldings have already been predicted by <I>mfold</I> , the <I>k</I><SUP><I>th</I></SUP>folding will have at least <I>W</I> base pairs that are at least a distance<I>W</I> from any of the base pairs in the first <I>k</I>-1 foldings. As <I>W</I>increases, the number of predicted foldings decreases. If <I>W</I> is notspecified, <I>mfold</I> selects a value by default based on sequence length,as displayed in Table <A HREF="#WINDOW">3</A>.<BR><DIV ALIGN="CENTER"><A NAME="826">&#160;</A><TABLE><CAPTION><STRONG>Table 3:</STRONG>If `W' is not specified, <I> mfold</I> will chooseits value from this table based on sequence length. The user isencouraged to experiment with this parameter.</CAPTION><TR><TD><TABLE CELLPADDING=3 BORDER="1"><TR><TD ALIGN="CENTER"><B> Sequence length</B></TD><TD ALIGN="CENTER"><B> Default window size</B></TD></TR><TR><TD ALIGN="CENTER">1-29</TD><TD ALIGN="CENTER">0</TD></TR><TR><TD ALIGN="CENTER">30-49</TD><TD ALIGN="CENTER">1</TD></TR><TR><TD ALIGN="CENTER">50-119</TD><TD ALIGN="CENTER">2</TD></TR><TR><TD ALIGN="CENTER">120-199</TD><TD ALIGN="CENTER">3</TD></TR><TR><TD ALIGN="CENTER">200-299</TD><TD ALIGN="CENTER">5</TD></TR><TR><TD ALIGN="CENTER">300-399</TD><TD ALIGN="CENTER">7</TD></TR><TR><TD ALIGN="CENTER">400-499</TD><TD ALIGN="CENTER">8</TD></TR><TR><TD ALIGN="CENTER">500-599</TD><TD ALIGN="CENTER">10</TD></TR><TR><TD ALIGN="CENTER">600-699</TD><TD ALIGN="CENTER">11</TD></TR><TR><TD ALIGN="CENTER">700-799</TD><TD ALIGN="CENTER">12</TD></TR><TR><TD ALIGN="CENTER">800-1199</TD><TD ALIGN="CENTER">15</TD></TR><TR><TD ALIGN="CENTER">1200-1999</TD><TD ALIGN="CENTER">20</TD></TR><TR><TD ALIGN="CENTER"><IMG WIDTH="16" HEIGHT="28" ALIGN="MIDDLE" BORDER="0" SRC="img97.gif" ALT="$\geq$">2000</TD><TD ALIGN="CENTER">25</TD></TR></TABLE></TD></TR></TABLE></DIV><BR><P>MAXBP :   A base pair <I>i</I>.<I>j</I> will not be allowed to form (inlinear RNA) if <!-- MATH: $j-i > MAXBP$ --><I>j</I>-<I>i</I> &gt; <I>MAXBP</I>. For circular RNA, a base pair <I>i</I>.<I>j</I>cannot form if <!-- MATH: $\min \{ j-i,n+i-j \} > MAXBP$ --><IMG WIDTH="237" HEIGHT="31" ALIGN="MIDDLE" BORDER="0" SRC="img98.gif" ALT="$\min \{ j-i,n+i-j \} > MAXBP$">.Thus small values ofMAXBP ensure that only short range base pairs will be predicted. Bydefault, <!-- MATH: $MAXBP = +\infty$ --><IMG WIDTH="122" HEIGHT="29" ALIGN="MIDDLE" BORDER="0" SRC="img99.gif" ALT="$MAXBP = +\infty$">,indicating no constraint.<P>MAX :   This is the maximum number of foldings that <I>mfold</I> will compute (50 by default). It is better to limit the number offoldings by careful selection of the P and W parameters.<P>ANN :   This parameter currently takes on 3 values. 1. `none': secondary structures are drawn without any specialannotation. Letters or outline are in black, while base pairs are redlines or dots for GC pairs and blue lines or dots for AU and GUpairs. 2. `p-num' : Colored dots, colored base characters or acombination are used to display in each folding how well-determinedeach base is according to the P-num values in the `fold_name.ann' file.3. `ss-count' : Colored dots, colored base characters or acombination are used to display in each folding how likely a base isto be single-stranded according to sample statistics stored in the`fold_name.ss-count' file. Both 2. and 3. were recently described[<A HREF="node19.html#ZUKM9801">38</A>].<P>START :   A segment to be folded is selected from the entiresequence. START is the first base, and is 1 by default.<P>STOP :   This is the last base in the folded segment. It isthe entire sequence length by default.<P>REUSE :   This parameter is either N (no, the default) or Y(yes). <I>mfold</I> creates a large save file, `fold_name.sav' thatcontains all the input parameters and the arrays of minimum foldingenergies for all sub-fragments of the folded sequence. This file,especially for large sequences, is expensive to create. If REUSE is`Y', then a file named `fold_name.sav' should exist from a previousrun. You must specify the sequence file. Any (new) constraint file willbe ignored, since constraints from the initial folding will beused. Similarly, NA, LC, T, MAXBP, START and STOP are determined fromthe initial run. However, RUN_TYPE, P, W, MAX and ANN may be alteredto give different numbers of foldings, different <I>energy dotplots</I>, and/or different types of structure annotation.<P>Additional command line parameters for future development arediscussed in the section on ``Future plans''.<P><HR><!--Navigation Panel--><A NAME="tex2html151" HREF="node9.html"><IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="img/next_motif.gif"></A> <A NAME="tex2html148" HREF="node7.html"><IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="img/up_motif.gif"></A> <A NAME="tex2html142" HREF="node7.html"><IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="img/previous_motif.gif"></A> <A NAME="tex2html150" 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="tex2html152" HREF="node9.html">OUTPUT</A><B> Up:</B> <A NAME="tex2html149" HREF="node7.html">Running the programs</A><B> Previous:</B> <A NAME="tex2html143" HREF="node7.html">Running the programs</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>
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