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