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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>Software platforms and environment</TITLE><META NAME="description" CONTENT="Software platforms and environment"><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="node5.html"><LINK REL="previous" HREF="node3.html"><LINK REL="up" HREF="FEBS98-html.html"><LINK REL="next" HREF="node5.html"></HEAD><BODY BGCOLOR=#FFDEAD TEXT=#202020 LINK=#800000 ALINK=#ffff00 VLINK=#353976><!--Navigation Panel--><A NAME="tex2html102" HREF="node5.html"><IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="img/next_motif.gif"></A> <A NAME="tex2html99" HREF="FEBS98-html.html"><IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="img/up_motif.gif"></A> <A NAME="tex2html93" HREF="node3.html"><IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="img/previous_motif.gif"></A> <A NAME="tex2html101" 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="tex2html103" HREF="node5.html">Loops and Nearest neighbor</A><B> Up:</B> <A NAME="tex2html100" HREF="FEBS98-html.html">Algorithms and Thermodynamics for</A><B> Previous:</B> <A NAME="tex2html94" HREF="node3.html">Introduction</A><BR><BR><!--End of Navigation Panel--><H1><A NAME="SECTION00040000000000000000">Software platforms and environment</A></H1><P>The <I>mfold</I> package [<A HREF="node19.html#ZUKM8901">16</A>,<A HREF="node19.html#JAEJ8901">17</A>,<A HREF="node19.html#JAEJ9001">18</A>,<A HREF="node19.html#ZUKM9401">19</A>] consistsof a group of programs written in Fortran or C, and a group of Bourneshell or Perl scripts. All of these programs and scripts run in a Unixenvironment. The <I>mfold</I> software is currently running on a number ofdifferent platforms, as indicated in Table <A HREF="#PLATFORM">1</A>.<BR><DIV ALIGN="CENTER"><A NAME="809"> </A><TABLE><CAPTION><STRONG>Table 1:</STRONG><I> mfold</I> runs on a variety of Unixplatforms. The ones shown have been tested by the first author.</CAPTION><TR><TD><TABLE CELLPADDING=3 BORDER="1"><TR><TD ALIGN="LEFT"><B> Operating System</B></TD><TD ALIGN="LEFT"><B> Hardware</B></TD></TR><TR><TD ALIGN="LEFT">Irix</TD><TD ALIGN="LEFT">SGI</TD></TR><TR><TD ALIGN="LEFT">Solaris</TD><TD ALIGN="LEFT">Sun SPARC</TD></TR><TR><TD ALIGN="LEFT">Ultrix</TD><TD ALIGN="LEFT">Dec Alpha</TD></TR><TR><TD ALIGN="LEFT">Solaris</TD><TD ALIGN="LEFT">Intel</TD></TR><TR><TD ALIGN="LEFT">Linux</TD><TD ALIGN="LEFT">Intel</TD></TR></TABLE></TD></TR></TABLE></DIV><BR><P>In addition, some of the core programs of <I>mfold</I> have been translatedinto C++ and the resulting software is running on Windows 98/WindowsNT (Intel hardware) with a point and click interface that usesproprietary Microsoft windowing tools. This program is called <I>RNAstructure</I>[<A HREF="node19.html#MATD9801">20</A>]. <P> Up to version 2.2, the programs in <I>mfold</I> were interactive andhad to be run individually. Versions 2.3 and 3.0 provide a simplecommand line interface, as described below, although it is stillpossible to run individual programs interactively or, for that matter,to write one's own scripts to link programs together in novelways. The RNA folding web server (<A HREF="http://www.bioinfo.rpi.edu/~zukerm/rna/form1.cgi")<TT>www.bioinfo.rpi.edu/<code>~</code>zukerm/rna/form1.cgi</TT>)</A>provides an HTML interface to <I>mfold</I> that uses a similar, butnot identical script. This server will be described elsewhere. It'smain advantage is that anyone with a web browser can use it.<P>An early version of <I>mfold</I> (2.0) was ported to run on Maccomputers. It lacked the <I>energy dot plot</I> and could only fold about 350 bases. Weno longer recommend its further use, especially since the energyparameters it uses have not been updated. The current <I>mfold</I> version3.0 runs in command line mode under Windows, but this implementationrequires a type of Unix emulation program to be run.<P>Two Unix ``environment variables'' must be defined for <I>mfold</I> tofunction. The first, <I>MFOLDBIN</I>, defines the directory where allthe executable files for <I>mfold</I> are stored. The second, <I>MFOLDLIB</I>, defines the directory containing all the free energy andother data files. Dynamic memory allocation is not yet available for<I>mfold</I> , and the largest fragment size that can be folded is defined bythe value of the <I>MAXN</I> parameter in the ``Makefile'' file.<P><HR><!--Navigation Panel--><A NAME="tex2html102" HREF="node5.html"><IMG WIDTH="37" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="next" SRC="img/next_motif.gif"></A> <A NAME="tex2html99" HREF="FEBS98-html.html"><IMG WIDTH="26" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="up" SRC="img/up_motif.gif"></A> <A NAME="tex2html93" HREF="node3.html"><IMG WIDTH="63" HEIGHT="24" ALIGN="BOTTOM" BORDER="0" ALT="previous" SRC="img/previous_motif.gif"></A> <A NAME="tex2html101" 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="tex2html103" HREF="node5.html">Loops and Nearest neighbor</A><B> Up:</B> <A NAME="tex2html100" HREF="FEBS98-html.html">Algorithms and Thermodynamics for</A><B> Previous:</B> <A NAME="tex2html94" HREF="node3.html">Introduction</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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