OUTPUT
Here is the plot from this session:
INPUT FILES
Domes accepts the base-by-base output file from FoldRNA as input. It only reads the fifth and sixth columns. Here is part of the file used in the example session:
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Domes uses an output file from FoldRNA to make a linear plot of a folded RNA molecule.
The program FoldRNA calculates an optimal RNA secondary structure and writes a base-by-base output file with the sequence name and the file name extension .connect. The Circles, Domes, DotPlot, Mountains, and Squiggles programs accept the FoldRNA output file and graph the RNA secondary structure. Circles, Domes, DotPlot, and Mountains make abstract representations, but the graphs they draw are easier to compare if you are looking for secondary structure motifs.
Domes represents a folded RNA sequence as a line with elliptical arcs connecting the bonded bases. This representation has the property that length of the arcs is proportional to the distance (along the primary structure) between the bases; hairpin, bulge, interior, and bifurcation loops are easily seen.
Here is a session using Domes to make a graph of the folding of Vi:Mcvsatrn5, as calculated in the example session for FoldRNA:
% domes Domes from what FOLDRNA file ? mcvsatrn5.connect When your LaserWriter attached to tty07 is ready, press <Return>. %
Here is the plot from this session:
Domes accepts the base-by-base output file from FoldRNA as input. It only reads the fifth and sixth columns. Here is part of the file used in the example session:
FOLDRNA of: gb_vi:mcvsatrn5 Check: 3205 from: 1 to: 334 October 13, 1996 11:22
Length: 334 Energy: -94.0
..
1 G 0 2 332 1
2 U 1 3 331 2
3 U 2 4 330 3
////////////////////////////
332 C 331 333 1 332
333 C 332 334 0 333
334 C 333 0 0 334
MFold predicts optimal and suboptimal secondary structures for an RNA molecule using the most recent energy minimization method of Zuker. PlotFold displays the optimal and suboptimal secondary structures for an RNA molecule predicted by MFold. FoldRNA predicts a single optimal secondary structure for an RNA molecule by the older method of Zuker. Circles, Domes, Mountains, Squiggles, and DotPlot all make graphic secondary structure representations with the .connect output file from FoldRNA and PlotFold.
The RNA secondary structure prediction algorithm and the folding energies used by MFold are more refined than the algorithm and energies used by FoldRNA. You cannot use the MFold energy files (see the LOCAL DATA FILES topic, below) with FoldRNA.
StemLoop finds all possible stems (inverted repeats) above some minimum quality that you can set, but StemLoop cannot recognize a structure with gaps (bulge loops or uneven bifurcation loops). The stems can be plotted with DotPlot.
Do not use FoldRNA with -REMOve if you want to plot the results!
The Wisconsin Package must be configured for graphics before you run any program with graphics output! If the % setplot command is available in your installation, this is the easiest way to establish your graphics configuration, but you can also use commands like % postscript that correspond to the graphics languages the Wisconsin Package supports. See Chapter 5, Using Graphics in the User's Guide for more information about configuring your process for graphics.
If you need to stop this program, use <Ctrl>C to reset your terminal and session as gracefully as possible. Searches and comparisons write out the results from the part of the search that is complete when you use <Ctrl>C. The graphics device should stop plotting the current page and start plotting the next page. If the current page is the last page, plotters should put the pen away and graphic terminals should return to interactive mode.
All parameters for this program may be put on the command line. Use the parameter -CHEck to see the summary below and to have a chance to add things to the command line before the program executes. In the summary below, the capitalized letters in the parameter names are the letters that you must type in order to use the parameter. Square brackets ([ and ]) enclose parameter values that are optional. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.
Minimal Syntax: % domes [-INfile1=]mcvsatrn5.connect -Default Prompted Parameters: None Local Data Files: None Optional Parameters: -SHOwseq shows the sequence in the plot -NUMbering[=10] displays sequence numbers every 10th base -NOTICks suppresses the ticks and their numbers -DENsity=600 sets the number of bases per 100 platen units -MINortomajor=0.8 sets the ratio between the axes of the ellipse -RECtangles plots rectangles instead of ellipses -PEAks plots diamond peaks instead of ellipses All GCG graphics programs accept these and other switches. See the Using Graphics chapter of the USERS GUIDE for descriptions. -FIGure[=FileName] stores plot in a file for later input to FIGURE -FONT=3 draws all text on the plot using font 3 -COLor=1 draws entire plot with pen in stall 1 -SCAle=1.2 enlarges the plot by 20 percent (zoom in) -XPAN=10.0 moves plot to the right 10 platen units (pan right) -YPAN=10.0 moves plot up 10 platen units (pan up) -PORtrait rotates plot 90 degrees
This idea of representing optimal RNA secondary structures with circular graphs comes from the work of Nussinov et al. (SIAM Journal of Applied Math. 35; 68-82 (1978)) (see Circles). The extension of this idea by representing RNA secondary structure with elliptical arcs that intersect with a straight line and the name Domes both come from Professor Paul Kaesberg (unpublished). Domes was first implemented for the IBM PC by Professor Claire Rinehart of the University of Western Kentucky. The GCG implementation of Domes was written by John Devereux with assistance from Irv Edelman.
None.
The parameters listed below can be set from the command line. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.
prints the sequence below the number line.
This program tries to number the ticks on each axis at an interval that gives about three to six numbered ticks. Use this parameter to set the numbering interval to please yourself. You can suppress tick numbering altogether with -NONUMbering.
suppresses the ticks and their numbers. -TICks is the default.
sets the number of bases or amino acids per 100 platen units (PU). This is usually equivalent to the number of bases or amino acids per page. Output from different GCG graphics programs that are run at the same density can be compared by lining up the plots on a light box.
sets the aspect of the ellipses, rectangles, or diamonds by setting the ratio of the minor to major axes. The default is 0.8. A ratio of 1.0 makes the ellipses into perfect circles and the rectangles into squares. You can set an aspect ratio for the plot that pushes the label and the axis off the platen completely.
draws rectangles to connect the paired bases, instead of ellipses.
draws diamonds to connect the paired bases, instead of ellipses.
The parameters below apply to all GCG graphics programs. These and many others are described in detail in Chapter 5, Using Graphics of the User's Guide.
writes the plot as a text file of plotting instructions suitable for input to the Figure program instead of drawing the plot on your plotter.
draws all text characters on the plot using Font 3 (see Appendix I).
draws the entire plot with the pen in stall 1.
The parameters below let you expand or reduce the plot (zoom), move it in either direction (pan), or rotate it 90 degrees (rotate).
expands the plot by 20 percent by resetting the scaling factor (normally 1.0) to 1.2 (zoom in). You can expand the axes independently with -XSCAle and -YSCAle. Numbers less than 1.0 contract the plot (zoom out).
moves the plot to the right by 30 platen units (pan right).
moves the plot up by 30 platen units (pan up).
rotates the plot 90 degrees. Usually, plots are displayed with the horizontal axis longer than the vertical (landscape). Note that plots are reduced or enlarged, depending on the platen size, to fill the page.
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Licenses and Trademarks Wisconsin Package is a trademark of Genetics Computer Group, Inc. GCG and the GCG logo are registered trademarks of Genetics Computer Group, Inc.
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