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In [[bioinformatics]] a '''dot plot''' is a graphical method that allows the comparison of two [[Sequence (biology)|biological sequences]] and identify regions of close similarity between them. It is a type of [[recurrence plot]].
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One way to visualize the similarity between two protein or nucleic acid sequences is to use a similarity matrix, known as a dot plot. These were introduced by Gibbs and McIntyre in 1970<ref name="gibbs-mcintyre"/> and are two-dimensional matrices that have the sequences of the proteins being compared along the vertical and horizontal axes. For a simple visual representation of the similarity between two sequences, individual cells in the matrix can be shaded black if residues are identical, so that matching sequence segments appear as runs of diagonal lines across the matrix.
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