Nucleic Acid Dot Plots

The program requires two nucleic acid sequences, which can be pasted into the text boxes labeled DNA Number 1 and DNA Number 2. The two sequences can be, and often are, identical. RNA sequences can also be entered; U's are automatically converted to T's. Two options are available for loading of the two sequences:

• Click Demo DNA -> DNA1 button to retrieve a demonstration sequence and inserts it into the DNA 1 text box.
• Click Copy DNA1 -> DNA2 button to copy the sequence in the DNA 1 text box to the DNA 2 text box. This is useful for setting up to compare a sequence to itself and search for repeated regions.

Two user-defined parameters can be set to control production of the matrix:

• Window Size is number of bases in a sliding window that is moved along each sequence and compared to generate a single data point on the plot. Window size must be an odd number.
• Mismatch Limit determines how similar the two sequences in a window must be to "match". For example, if window size is 9 and mismatch limit is 2, then up to 2 mismatches in a 9 base window will still be classified as a match.

After filling each text box with a sequence and setting window size and mismatch limit, click the Plot button. Note that all messages, including error alerts, are displayed in the yellow text box.

Once a plot is generated, clicking on a point within it will generate a message describing the relative position (base number) in the two sequences.