Strings 2008 2 4

Visual comparison of strings

Humans are very good at identifying patterns visually. One of the first ways to compare biological sequences was to generate identity matrices and visualise them in a so called dot plot.

Computing of a dot plot

The two sequences correspond to the two dimensions of the matrix and each matrix element represents the outcome of the comparison between the two corresponding characters in the sequences. Identical character pairings are visualised by a black pixel while different characters are coloured white.

The figure below shows an example of a dot plot comparing two DNA sequencess.

INSERT FIGURE HERE

Discovery questions: Suppose that two sequences are identical except that a segment is inverted in one sequence, relative to the other sequence. Explain how such an inversion would look like in a dot plot. What would be the value of using a dot plot to compare a sequence to a second sequence, as well as the reverse compliment of the second sequence? Sketch a dot plot of two sequences which are identical except that a segment is deleted from the middle of one sequence and not the other.