The dotplot is a simple picture that gives an overview of the similarities between two sequences. Less obvious is its close relationship to alignments.
The dotplot is a table or matrix. The rows correspond to the residues of one sequence and the columns to the residues of the other sequence.
In its simplest form, the positions in the dotplot are left blank if the residues are different, and filled if they match. Stretches of similar residues show up
as diagonals in the upper left–lower right (northwest–southeast) direction. The dotplot gives a quick pictorial statement of the relationship between two sequences.
Obvious features of similarity stand out.
The most basic sequence alignment method is the dot matrix method, also known
as the dot plot method.
It is a graphiscal way of comparing two sequences in a two-dimensional matrix.
In a dot matrix, two sequences to be compared are written in the horizontal and vertical axes of the matrix.
The comparison is done by scanningeach residue of one sequence for similarity with all residues in the other sequence.
If a residue match is found, a dot is placed within the graph. Otherwise, the matrix
positions are left blank.
When the two sequences have substantial regions of similarity,
many dots line up to form contiguous diagonal lines, which reveal the sequence
alignment. If there are interruptions in the middle of a diagonal line, they indicate
insertions or deletions.
Parallel diagonal lines within the matrix represent repetitive
regions of the sequences
