OUTPUT
Here is the plot from this session:
INPUT FILES
Circles 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:
[ Program Manual | User's Guide | Data Files | Databases ]
Circles uses an output file from FoldRNA to make a circular Nussinov 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.
The circular graph plotted by Circles represents the sequence as a segment of a circle. You can set the radius and the angular width of one base so that plots of different secondary structures are strictly comparable. All of the bases that participate in stems are shown with arcs or chords connecting them; hairpin, bulge, interior, and bifurcation loops are easily seen.
Here is a session using Circles to make a graph of the folding of Vi:Mcvsatrn5, as calculated in the example session for FoldRNA:
% circles CIRCLES plot of what FOLDRNA output file ? mcvsatrn5.connect The maximum angle per base is 1.0629 degrees/base A typical value is about 2.0 degrees/base What angle per base (* 1.0629 *) ? What radius (* 45.0 *) ? When your LaserWriter attached to tty07 is ready, press <Return>. %
Here is the plot from this session:
Circles 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: % circles [-INfile1=]mcvsatrn5.connect -Default Prompted Parameters: -ANGleperbase=1.0629 degrees of arc given to each base -RADius=45.0 radius of circle Local Data Files: None Optional Parameters: -SHOwseq shows the sequence itself around the edge -NUMbering[=10] display sequence numbers every 10th base -NOTICks suppresses the ticks and their numbers -CHOrds connects paired bases with chords instead of circles 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)). Circular graphs were also used to illustrate the argument for Zuker's original paper describing FoldRNA (Nucl. Acids Res. 9(1); 133-148 (1981)). Circles was written by John Devereux and Yonah D. Karp. William Winsborough worked out the trigonometry for the GCG implementation of Circles.
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.
connects paired bases with straight lines. Normally Circles uses circular segments to connect bases that are paired.
prints the sequence itself around the circumference. -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.
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.
[ Program Manual | User's Guide | Data Files | Databases ]
Documentation Comments: doc-comments@gcg.com
Technical Support: help@gcg.com
Copyright (c) 1982, 1983, 1985, 1986, 1987, 1989, 1991, 1994, 1995, 1996 Gentics Computer Group, Inc. All rights reserved.
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.
All other product names mentioned in this documentation may be trademarks, and if so, are trademarks or registered trademarks of their respective holders and are used in this documentation for identification purposes only.
