DotPlot

For fast satisfaction, try comparing two neuronal nicotinic acetylcholine receptor subunit sequences from swissprot saved under the filenames a2 and a3. The interface is like any other Windows program. Use the File popup menu to load the horizontal sequence.
You get a dialog box listing all the files in the current directory. Select a2, then the program gives a SeqInfo dialog box, which tells you a little bit about the sequence you just loaded ie. its name, length, sequence format and whether its DNA, RNA or protein. Click OK. Then repeat for the vertical sequence, choosing a3.
As in the MSDOS version, there are two ways of calculating the dotplot, described in detail below. For a quick fix, use the Identities option on the Draw popup menu. The default parameters are a window size of 10 and a threshold of 6. This gives a diagonal line across your screen. Try tweaking the dotplot by clicking on Parameters and setting the threshold to 1. Pretty, isnt it? You can even see the three transmembrane regions in the middle of the protein and the final transmembrane at the C-terminus.
Try to find the internal repeats in a human epidermal growth factor receptor. To do this, load the sequence called egfr as both the horizontal and the vertical sequence. Then set the parameters as window=20 and threshold=1. Load the PAM250.MAT score matrix using the File popup menu "Open Matrix" option.
The DotPlot application was developed to be Dot plot analysis tool.