DotPlot makes a dot-plot with the output file from Compare or StemLoop.
Dot-plotting is the best way to see all of the structures in common between two sequences or to visualize all of the repeated or inverted repeated structures in one sequence. DotPlot is the second part of a two-part set of programs that generate dot-plots of the points of similarity between two sequences. (See Maizel and Lenk (1981) "Enhanced Graphic Matrix Analysis of Nucleic Acid and Protein Sequences" Proc. Natl. Acad. Sci. (USA) 78(12); 7665-7669.) Compare writes a point file with the coordinates of the points in common between two sequences. DotPlot plots those points on a plotter or a graphics terminal.
DotPlot calculates the minimum density in bases per 100 platen units along either axis that would allow all of the points to be plotted on a single page. At high densities (for example, 1,000 bases per 100 platen units), the dots will not be individually resolved.
You can select any density you want and DotPlot divides the plot into as many pages as it takes to plot the whole file. Look at the output suggestions below for more help on the format.
The plot from this session made with the Apple LaserWriter is reproduced in the first figure at the end of this program entry. The second figure shows a plot of a word comparison of the same two sequences, using a word size of 8. The input point file for the second figure is hpr-word.pnt.
DotPlot accepts as input a point file created by the Compare program. StemLoop can create a point file acceptable as input to DotPlot if you choose to output the stems as points.
Compare and StemLoop generate files with the points to actually be plotted by DotPlot. BestFit and Gap align regions of interest identified with dot-plots and present you with a base-by-base alignment with gaps inserted.
No more than 200,000 points can be plotted. The density is measured in symbols per 100 platen units. The Hewlett Packard 7475 plotter plots from 350 to 450 points per minute and resolves the points at densities below 1,000 bases per 100 platen units. The Hewlett Packard 7550 plotter plots about 1,000 points per minute.
DotPlot gives you the option of extending a plot over several pages. If the chosen point density requires more than one page for plotting, the pages are all marked with the date and time so that they can be associated. To see all of the dots distinctly, you should plot 1,000 bases/100 platen units or less. A good plot does not have more than a few thousand points.
Each page of a multi-page plot is marked with the date and time. Each axis is marked with a number that tells how many pages away from the origin the axis is. For instance, the lower-left page is marked with a '1' on both axes. The upper-right page of a nine-page plot with three divisions on each axis would be marked with a '3' on both axes. -AUTOFeed causes plotters with automatic paper feed to put in new paper automatically.
If the sequences compared are the same in both range and checksum, then only the points above the diagonal are plotted and only pages with at least one possible point above the diagonal are shown. This feature can be canceled with -ALL.
You can plot two comparisons on the same piece of paper. For instance, you can compare proteins and nucleic acids on the same sheet by plotting on the same page. The optional parameters -NOLABel, -SYMbol, -NOCAPtion, and -POIntcolor can help you make the second plot contrast with the first. -NOUNLoad is useful with Hewlett Packard plotters -- it keeps GCG programs from unloading the paper after each plot.
You can set the parameters listed below from the command line. For more information, see "Using Program Parameters" in Chapter 3, Using Programs in the User's Guide.