Bioinformatics explained: Dot plots

Dot plots are two-dimensional plots where the x-axis and y-axis each represents a sequence and the plot itself shows a comparison of these two sequences by a calculated score for each position of the sequence. If a window of fixed size on one sequence (one axis) match to the other sequence a dot is drawn at the plot. Dot plots are one of the oldest methods for comparing two sequences [Maizel and Lenk, 1981].

The scores that are drawn on the plot are affected by several issues.