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Mountains uses an output file from FoldRNA to make a plot of an RNA secondary structure.
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.
Mountains makes a graph that looks like a mountain range. Horizontal striations upon a particular peak are bonds between bases, and vertical links between the horizontal striations represent stems.
To make your graph more readable, you can suppress the base labels and decrease horizontal density to create multi-page plots.
Here is a session using Mountains to make a graph of the folding of Vi:Mcvsatrn5, as calculated in the example session for FoldRNA:
% mountains
MOUNTAINS of what FOLDRNA output file ? mcvsatrn5.connect
The minimum density for a one page plot is: 256.9 bases/100pp
A typical density is 200 bases / 100 platen units
What density would you like (* 256.9 *) ?
MOUNTAINS will take 1 pages. Would you like to:
P)lot the statistics
D)ifferent density
Q)uit
Please select one (* P *):
When your LaserWriter attached to tty07 is ready, press <Return>.
%
If you are reading the Program Manual, the plot from this session is shown in the figure at the end of this program entry.
Mountains 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 secondary structures of large molecules may make crowded graphs. Mountains allows you to create a more readable plot in two different ways. By setting the optional parameter -DENsity smaller than the minimum density for a one-page plot, you can create multi-page plots with the information spread out. You can use -SHOwseq to replace the dots around the plot with letters showing the bases.
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: % mountains [-INfile=]mcvsatrn5.connect -Default Prompted Parameters: -DENsity=256.9 bases per 100 platen units along the X axis Local Data Files: None Optional Parameters: -SHOwseq displays the sequence on the edge of the mountains -NUMbering[=10] displays sequence numbers every 10th base -NOTICks suppress the ticks and their numbers -STEMdepth=27 number of stems on the Y axis of each page 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
Inspiration for this program came from Hogeweg and Hesper, Nucl. Acids Res. 12; 67-74 (1984). Mountains was written by Verne A. Luckow and Yonah D. Karp.
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.
replaces the dots around the plot with letters showing the bases. -NOSHOwseq is the default.
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.
is the number of stems that can be stacked on the y axis on each page. The default is the number calculated to fit on one page.
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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