Dot plots

Dot plots provide a powerful visual comparison of two sequences. Dot plots can also be used to compare regions of similarity within a sequence.

A dot plot is a simple, yet intuitive way of comparing two sequences, either DNA or protein, and is probably the oldest way of comparing two sequences [Maizel and Lenk, 1981]. A dot plot is a 2 dimensional matrix where each axis of the plot represents one sequence. By sliding a fixed size window over the sequences and making a sequence match by a dot in the matrix, a diagonal line will emerge if two identical (or very homologous) sequences are plotted against each other. Dot plots can also be used to visually inspect sequences for direct or inverted repeats or regions with low sequence complexity. Various smoothing algorithms can be applied to the dot plot calculation to avoid noisy background of the plot. Moreover, various substitution matrices can be applied in order to take the evolutionary distance of the two sequences into account.