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Squiggles 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.
Squiggles creates a representation similar to what you might draw by hand; that is, bonds formed between bases are drawn as chords. The entire structure looks like an airport or intersecting railroad tracks. The spider-like graph plotted by Squiggles represents the sequence as bases connected by chords. Bases are shown participating in stems, as well as in hairpin, bulge, interior and bifurcation loops. These structures are easily seen in Squiggles.
To make your graph more readable, you can label the bases, show sequence numbers at set intervals, and pivot up to nine stems. You can also change the character height for the number and base labels.
Here is a session using Squiggles to make a graph of the folding of Vi:Mcvsatrn5, as calculated in the example session for FoldRNA:
% squiggles SQUIGGLES of what FOLDRNA output file ? mcvsatrn5.connect 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.
Squiggles 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 squiggle plot tends to look more significant as the molecule gets larger. Do not be deceived -- the loops are simply given less room so the stems look longer and more continuous!
The secondary structures of large molecules may make crowded graphs. Squiggles has an optional parameter -PIVOt that bends up to nine substructures to make the representation more readable. -SEQHeight can be changed to allow the base and number labels to conform to the amount of information on the graph.
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: % squiggles [-INfile=]mcvsatrn5.connect -Default
Prompted Parameters: None
Local Data Files: None
Optional Parameters:
-SHOwseq show the sequence in the plot
-SHOwseq[=32,45] specify a range of the sequence to be shown
-SEQHeight=0.9 height (in platen units) for sequence display and
numbering
-NUMbering [=10] display sequence numbers every 10th base
-PIVOt =i,j,theta pivot the substructure starting at i and ending at
j theta degrees
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
Squiggles originates with the work of Osterburg and Sommer (Comput. Programs in Biomed. 13; 101-109 Figure 7 (1981)). The subroutine DRWFLD was taken from a FORTRAN translation of their program and extensively revised by Verne 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.
labels the bases. -SHOwseq without any optional values provides a labeling letter for each base. Appending values to the -SHOwseq parameter allows you to label only a particular substructure of interest. -NOSHOwseq is the default.
is the character size for base and number labels. The default is .9 platen units, and the allowable range is from .2 to 5.0.
puts a sequence number as a label at every fifth base. The default interval is 10. -NONUMbering suppresses the numbering.
allows you to pivot stems or other substructures to make the graph more readable and fix collision between stems. The first number, where the pivoting begins, should be the underarm of an arm to be bent. The second number should be the corresponding shoulder. The third number is the number of degrees (-360 to 360) the structure should be rotated counterclockwise.
Overlapping intervals may be used, if you wish, to pivot a large structure at one angle and a smaller portion of that structure at another angle.
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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