Explanation of output formats

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. The consortium has a long history of working together to address this issue: the current proposal is the culmination of discussions (formal and informal) that began at the Madison meeting of the RNA Society in 1998. The consortium includes a reasonably broad representation of those active in the RNA informatics field, a feature that increases the chances that this proposed format will be accepted by the RNA community at large. 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) Abstract

PostScript & PDF: 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. PDF (Portable Document Format) was also created by Adobe Systems, and goes far beyond PostScript. See Adobe's own description at PostScript vs. PDF.

.jpg or .png: A graphics file that ends with the suffix .jpg or .png should be displayed directly on the page of your web browser. These formats can also be displayed externally using a variety of programs.

.ct file: The '.ct file' contains the nucleic acid sequence and base pairing information from which a structure plot may be computed. The web folding servers use the .ct files together with the "sir_graph" program by D. Stewart and M. Zuker to create the structure output files. The "sir_graph" software is available within the mfold_util suite of programs.

Vienna: This output format is used in the "Vienna RNA Package". It consists of two lines. The first line contains the sequence as a continuous string of characters. The second line contains only the characters "(", ")" and ".". A base underlined by "(" is the 5' base in a base pair and a base underlined by ")" is the 3' base in a base pair. A base underlined by "." is not paired. The lack of pseudoknots in the secondary structure ensures that this notation defines a unique folding.

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 used by Accelrys' GCG) software. This file 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.