DotPlot

DotPlot is a handy tool for comparing sequences, especially if you're looking at two neuronal nicotinic acetylcholine receptor subunit sequences from SwissProt. You can easily open your files labeled a2 and a3. The interface feels familiar, just like any other Windows program you might use.

Loading Your Sequences

To get started, click on the File menu to load the horizontal sequence. A dialog box will pop up showing all the files in your current folder. Select a2, and then you'll see a SeqInfo dialog box. This little box gives you info about the sequence, like its name, length, format, and whether it's DNA, RNA, or protein. After you check that out, just hit OK and do the same for your vertical sequence by choosing a3.

Calculating the DotPlot

Once you have both sequences loaded, you can calculate the dot plot. There are two methods to do this—let's start with an easy one! Click on the Draw menu and choose Identities. The default settings give you a window size of 10 and a threshold of 6. You'll notice a nice diagonal line across your screen! Want to make it more interesting? You can tweak it by clicking on Parameters and setting that threshold down to 1. Now you'll see some cool patterns like three transmembrane regions right in the middle of the protein!

Finding Internal Repeats

If you're curious about internal repeats in something like a human epidermal growth factor receptor (EGFR), here's what to do: Load that sequence as both your horizontal and vertical options. Set your parameters to window=20 and threshold=1 for more detailed insights. Don't forget to load up the PAM250.MAT score matrix by going back to the File menu and selecting 'Open Matrix'.

A Quick Summary of DotPlot

The DotPlot application is designed specifically for dot plot analysis. It's user-friendly while offering powerful features for analyzing sequences effectively!