c

 

 
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This article is about the biological sequences comparison plot. For the statistical plot, see Dot
plot (statistics).

A 

(aka 


or

 

) is a graphical method that allows the
comparison of two biological sequences and identify regions of close similarity between them. It
is a kind of recurrence plot.

 


[hide]

RÊ ½ Introduction
RÊ Ô Example
RÊ  See also
RÊ G References
RÊ u External links

°



 
The simplest way to visualize the similarity between two protein sequences is to use a similarity
matrix, known as a dot plot. These were introduced by Philips in the ½
s[÷

] and are
two-dimensional matrices which 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.

Some idea of the similarity of the two sequences can be gleaned from the number and length of
matching segments shown in the matrix. Identical proteins will obviously have a diagonal line in
the center of the matrix. Insertions and deletions between sequences give rise to disruptions in
this diagonal. Regions of local similarity or repetitive sequences give rise to further diagonal
matches in addition to the central diagonal. Because of the limited protein alphabet, many
matching sequence segments may simply have arisen by chance. One way of reducing this noise
is to only shade runs or 'tuples' of residues, e.g. a tuple of  corresponds to three residues in a
row. This is effective because the probability of matching three residues in a row by chance is
much lower than single-residue matches. It can be seen from Figures .h,c that the number of
diagonal runs in the matrix has been considerably reduced by looking for Ô-tuples or -tuples.

Dot Plots are one of the oldest ways of comparing two sequences.[÷

] They compare two
sequences by organizing one sequence on the x-axis, and another on the y-axis, of a plot. When
the residues of both sequences match at the same location on the plot, a dot is drawn at the
corresponding position. Note, that the sequences can be written backwards or forwards, however
the sequences on both axes must be written in the same direction. Also note, that the direction of
the sequences on the axes will determine the direction of the line on the dot plot. Once the dots
have been plotted, they will combine to form lines. The closeness of the sequences in similarity
will determine how close the diagonal line is to what a graph showing a curve demonstrating a
direct relationship is. This relationship is affected by certain sequence features such as frame
shifts, direct repeats, and inverted repeats. Frame shifts include insertions, deletions, and
mutations. The presence of one of these features, or the presence of multiple features, will cause
for multiple lines to be plotted in a various possibility of configurations, depending on the
features present in the sequences. A feature that will cause a very different result on the dot plot
is the presence of low-complexity region/regions. Low-complexity regions are regions in the
sequence with only a few amino acids, which in turn, causes redundancy within that small or
limited region. These regions are typically found around the diagonal, and may or may not have
a square in the middle of the dot plot.

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A DNA dot plot of a human zinc finger transcription factor (GenBank ID NM_Ô), showing
regional self-similarity. The main diagonal represents the sequence's alignment with itself; lines
off the main diagonal represent similar or repetitive patterns within the sequence.

Example of a dot plot for comparing two simple protein sequences:

½.Ê All cells associated with identical residue pairs between the sequences are shaded black;
Ô.Ê only those cells associated with identical tuples of two residues are shaded black; and
.Ê only cells associated with tuples of three are shaded and the optimal path through the
matrix has been drawn.

This is constrained to be within the window given by the two black lines parallel to the central
diagonal. An alternative high-scoring path is also shown.