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<head><title>Explanation of Output Formats</title></head><!--body bgcolor="#60ad97" text="#111111" link="#800000" vlink="#806000" alink="#0000dd"--><body BACKGROUND="back.gif" text="#111111" link="#800000" vlink="#806000" alink="#0000dd"-->Michael Zuker, Rensselaer Polytechnic Institute<hr><font size=2><i><a href="#TXT">Text Output</a> |<a href="#RNAML"><i>RNAML</i> Syntax</a> |<a href="#PS">PostScript</a> |<a href="#GIF">gif</a> |<a href="#CT">ct file</a> |<a href="#MAC">Mac ct</a> |<a href="#GCG">GCG connect</a> |<a href="#XRNA">XRNA ss</a></i></font><hr><dl><a name=TXT><dt> <img src="l_purple.gif" hspace=5><font size=5 color=#003000><i>Text Output</i></font></a> <p><dd> This is the original form of output. All computed structures areplaced in the same file. The hypertext link to the<i>i<sup>th</sup></i> structure is '<u>Structure i</u>'. This simpleform of output is useful for small structures. It can also be a goodreference for large foldings where only the outline has been plotted.<hr size=3 noshade> <p><a name=RNAML><dt> <img src="l_brown.gif" hspace=5><font size=5 color=#003000><i>RNAML Syntax</i></font></a> <p><dd> The RNAML (RNA Markup Language) was developed by a consortium ofinvestigators and is a proposed syntax for RNA information files.A description was published in 2002: <blockquote>A. Waugh, P. Gendron, R. Altman, J.W. Brown, D. Case, D. Gautheret,S.C. Harvey, N. Leontis, J. Westbrook, E. Westhof, M. Zuker, &F. Major <br> RNAML: A standard syntax for exchanging RNAinformation.<br> <i>RNA</i> <b>8 (6)</b>, 707-717, (2002) <a href="http://www.rnajournal.org/cgi/content/abstract/8/6/707">Abtract</a> </blockquote><hr size=3 noshade> <p><a name=PS><dt> <img src="l_green.gif" hspace=5><font size=5 color=#003000><i>PostScript</i></font></a> <p><dd> PostScript is a programming language that is used to describeoutput for printing and display. It was developed by Adobe Systems. Itis common to have PostScript capability on most printers. Programssuch as <a href="http://www.cs.wisc.edu/~ghost/">Ghostscript, Ghostview and GSview</a> can be used to displayPostScript files. Another program named "ggv" is also available.<hr size=3 noshade> <p><a name=GIF><dt> <img src="l_cyan.gif" hspace=5><font size=5 color=#003000><i>.gif</i></font></a> <p><dd> A graphics file that ends with the suffix .gif, .jpeg or .pngshould be displayed directly on the page of your web browser. Theseformats can also be displayed externally using a program such as 'xv'.<hr size=3 noshade> <p><a name=CT><dt> <img src="l_grey.gif" hspace=5><font size=5 color=#003000><i>.ct file</i></font></a> <p><dd> The '.ct file' contains the nucleic acid sequence and basepairing information from which a structure plot may be computed. Themfold software and mfold web servers use the "sir_graph_ng" program tocreate Postscript, jpg and png images from .ct files. "sir_graph_ng"is part of the mfold_util package that may be obtained <ahref="http://www.bioinfo.rpi.edu/~zukerm/export/"> here.</a>. Take themost recent version.<hr size=3 noshade> <p><a name=MAC><dt> <img src="l_blue.gif" hspace=5><font size=5 color=#003000><i>Mac .ct</i></font></a> <p><dd> This is a variant of the .ct file designed for the Mac program'loopdloop' by Don Gilbert. It may be obtained from the <a href="http://iubio.bio.indiana.edu/"><b>IUBio Archive</b></a> at the University of Indiana. Go to the<a href="http://iubio.bio.indiana.edu/IUBio-Software%2bData/molbio/loopdloop/"><i>loopDloop</i></a> directory and take either the older version inmac-app directory or the newer java version in the java directory.<hr size=3 noshade> <p><a name=GCG><dt><img src="l_red.gif" hspace=5><font size=5 color=#003000><i>GCG .connect</i></font></a> <p><dd> This is another variant of the .ct file that can be used with the<a href="http://www.accelrys.com/">DS GCG</a> package from Accelrys.These files can be used as input to any of the GCG programs that plotRNA secondary structure: <i>Circles, Domes, Mountains and Squiggles</i>.<hr size=3 noshade> <p><a name=XRNA><dt><img src="l_yellow.gif" hspace=5><font size=5 color=#003000><i>XRNA ss</i></font></a> <p><dd> This is an input file for the XRNA program by Bryn Weiser andHarry Noller. The new Java version is available from UC Santa Cruz <ahref="http://rna.ucsc.edu/rnacenter/">RNA Center</a> web site: <ahref="http://rna.ucsc.edu/rnacenter/xrna/xrna.html">XRNA</a>. The<i>ss</i> file can be regarded as an expanded <i>ct</i> file. Itcontains base and connect information as well a coordinates forplotting the bases.</dl> <p><center><img src="end2.gif"></center><pre></pre></body>⌨️ 快捷键说明
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