Sequence Dot Plot

VectorBuilder’s Sequence Dot Plot tool allows you to identify regions of close similarity between two DNA or RNA sequences by comparing them in a two-dimensional plot. The two sequences being compared are arranged on the top X and left Y axes of a two-dimensional matrix and dots are used to represent the coordinates at which both sequences match. As a result, a dot plot of two identical sequences consists of a single diagonal line in the center of the matrix. In addition, dot plots can help identify regions with direct or inverted repeats, frameshifts, sequence inversions and low complexity within sequences. For example, when a sequence containing direct repeats is compared against itself, it results in a dot plot containing multiple diagonal lines representative of the repetitive regions within the sequence.

A major limitation of using dot plots to compare sequences is that they are susceptible to significant background noise, especially when comparing large sequences with a high degree of similarity which makes identification of similar regions on the plot difficult. Background noise can be reduced by setting a window size and a mismatch limit which allows the tool to compare the two sequences within the set window size and assign a dot only when a certain number of matches occur within that window.