Michael Zuker, Rensselaer Polytechnic Institute
Text Output | RNAML Syntax | PostScript | gif | ct file | Mac ct | GCG connect | XRNA ss
Text Output

This is the original form of output. All computed structures are placed in the same file. The hypertext link to the ith 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)     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.

.gif

A graphics file that ends with the suffix .gif or .jpeg 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 web folding servers use the .ct files with the 'naview' program by Bruccoleri & Heinrich to create the structure output files. This package may be obtained here.

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 created by the Genetics Computer Group (GCG) of Madison, WI. 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.