The directories contain results from RNA foldings calculated by mfold
The graphics and connectivity information are given for each of the
MinE (global minimum free energy) structure of the 11 picornaviruses
The formats of the "connect" and "region" text files
created by mfold can be found in the mfold
manual. These files are contained in directories CONNECT
* A "connect" file describes linearly, one base per line,
the connectivity of each base within the stucture.
* A "region" file summarizes information for each helix: begining
and ending base, length and free energy contributed by that helix.
The sequences used for the folding are located in the SEQ
directory in a simple plain text file 60 columns accross and with no
directory contains plain text files formated with the GCG "figure"
plot commands. These files can be used as input source to create graphics
output with either the Macintosh stand-alone program GCGFigure
available free at the GCG
site. The program allows users to zoom onto a particular portion
of the (color) display and can generate screen-resolution (72 dpi) Macintosh
PICT files or print to a PostScript(R) file.
Alternatively the GCG program FIGure can be used on a VMS or UNIX workstation
where the GCG package is installed. Graphics output will depend on chosen
The "figure" files can be opened with a word processor for
inspection. After the header, comment lines (starting with a !) show
the base number and the percentage of the "normalized" pnum
value x 1000. The previous line shows the color (.nc 1 = black, .nc
2 = green, .nc 4 = red). The very bottom of the file indicates the number
of bases for each color in the file.
For example the first base of cb3 has a normalized P-num of 4.395% and
is therefore green (previous line is .nc 2) since it is less than the
3% cut off. All P-num are derived from a .plot file generated by mfold
for 12Kcal over the MinE energy.
For more detailed explanations on how to use these files for graphics
output please refer to: http://www.virology.edu/acp/RNAFolds/FIGURE
Finding All Suboptimal Foldings of an RNA Molecule.
Science 244, 48-52 (1989)
J.A. Jaeger, D.H. Turner & M. Zuker
Predictions of Secondary Structures for RNA.
Proc. Natl. Acad. Sci. USA 86, 7706-7710 (1989)
Rowe C.L., Fleming J.O., Nathan M.J., Sgro J.-Y.,
Palmenberg AC. andBaker SC.
Generation of coronavirus spike deletion variants
by high-frequency recombination at regions of predicted RNA secondary
J. Virol. 71, 6183-6190 (1997)