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.
- Scoring matrix for distance correction.
Scoring matrices (BLOSUM and PAM) contain substitution scores for every combination of two amino acids. Thus, these matrices can only be used for dot plots of protein sequences.
- Window size
The single residue comparison (bit by bit comparison(window size = 1)) in dot plots will undoubtedly result in a noisy background of the plot. You can imagine that there are many successes in the comparison if you only have four possible residues like in nucleotide sequences. Therefore you can set a window size which is smoothing the dot plot. Instead of comparing single residues it compares subsequences of length set as window size. The score is now calculated with respect to aligning the subsequences.
The dot plot shows the calculated scores with colored threshold. Hence you can better recognize the most important similarities.