Explanation of Output Formats

Michael Zuker, Rensselaer Polytechnic Institute

Text Output: This is the original form of output. All computed structures are placed in the same file. The hypertext link to the i^th structure is 'Structure i'. This simple form of output is useful for small structures. It can also be a good reference for large foldings where only the outline has been plotted.
RNAML Syntax: The RNAML (RNA Markup Language) was developed by a consortium of investigators and is a proposed syntax for RNA information files. A description was published in 2002:
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
RNAML: A standard syntax for exchanging RNA information.
RNA 8 (6), 707-717, (2002) Abtract
PostScript: PostScript is a programming language that is used to describe output for printing and display. It was developed by Adobe Systems. It is common to have PostScript capability on most printers. Programs such as Ghostscript, Ghostview and GSview can be used to display PostScript files. Another program named "ggv" is also available.
.gif: A graphics file that ends with the suffix .gif, .jpeg or .png should be displayed directly on the page of your web browser. These formats can also be displayed externally using a program such as 'xv'.
.ct file: The '.ct file' contains the nucleic acid sequence and base pairing information from which a structure plot may be computed. The mfold software and mfold web servers use the "sir_graph_ng" program to create Postscript, jpg and png images from .ct files. "sir_graph_ng" is part of the mfold_util package that may be obtained here.. Take the most recent version.
Mac .ct: This is a variant of the .ct file designed for the Mac program 'loopdloop' by Don Gilbert. It may be obtained from the IUBio Archive at the University of Indiana. Go to the loopDloop directory and take either the older version in mac-app directory or the newer java version in the java directory.
GCG .connect: This is another variant of the .ct file that can be used with the DS GCG package from Accelrys. These files can be used as input to any of the GCG programs that plot RNA secondary structure: Circles, Domes, Mountains and Squiggles.
XRNA ss: This is an input file for the XRNA program by Bryn Weiser and Harry Noller. The new Java version is available from UC Santa Cruz RNA Center web site: XRNA. The ss file can be regarded as an expanded ct file. It contains base and connect information as well a coordinates for plotting the bases.