RNA Folds: Picornavirus Folding Files

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Picornavirus Folding Files
Palmenberg A. C. and Sgro J.Y. (1997)
Seminars in Virology 8:231-241


The directories contain results from RNA foldings calculated by mfold (M. Zuker).

The graphics and connectivity information are given for each of the MinE (global minimum free energy) structure of the 11 picornaviruses studied.

Description files

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 and REGION respectively. Briefly:

* 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 other symbols.

Graphics files

The FIGURE 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 settings.

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
REFERENCES

PROGRAM MFOLD:
   M. Zuker
   On Finding All Suboptimal Foldings of an RNA Molecule.
   Science 244, 48-52 (1989)
PNUM:
   J.A. Jaeger, D.H. Turner & M. Zuker
   Improved Predictions of Secondary Structures for RNA.
   Proc. Natl. Acad. Sci. USA 86, 7706-7710 (1989)
PNUM NORMALIZED:
   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 structure.
   J. Virol. 71, 6183-6190 (1997)

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