Biomedical Engineering Reference
In-Depth Information
Dot Matrix Analysis
Because alignment by visual inspection of linear sequences hundreds of characters or more in length
was impractical, researchers developed a more visually intuitive method of pattern detection called
the dot matrix method. This method of sequence alignment, which was first performed manually and
then computerized, makes the similarities in patterns more obvious to visual inspection. Using this
method, one sequence appears along the top, and one along the side of the matrix, and a dot is
placed at the intersection of matching character pairs. Contiguous diagonal rows of dots indicate
sequences of matching pairs, as in the dot matrix plot of sequences (G) and (H) in
Figure 8-3
.
Figure 8-3. Dot Matrix Pairwise Alignment of Nucleotide Sequences (G—top)
and (H—side). Diagonal sequences of dots indicate areas of contiguous
sequences of aligned pairs. In a typical plot, there may be hundreds of
characters in each sequence.
The dot matrix pattern for a pair of perfectly matching sequences would include a contiguous
sequence of dots running down the center diagonal of the matrix. However, this pattern is rarely
seen in practice. Most often, the diagonal patterns are difficult to discern without additional
processing. In addition to the use of color and other methods of highlighting matching sequences, a
variety of filters are often applied to the data. For example, a common filter is a combination of
window and stringency. The window refers to the number of data points examined at a time, while
the stringency is the minimum number of matches required within each window.
With a filter in which the window size is set to 2 and the stringency to 1, a dot is printed at a matrix
position only if 1 out of the next 2 positions is identified, as in
Figure 8-4
. Similarly, with a window
size of 6 and a stringency of 3, a dot would be printed at a matrix position only if 3 of the next 6
