How do I interpret the plot made by the SEQDOTPLOT function in the Bioinformatics Toolbox 1.1.1 (R14SP1)?

When I use SEQDOTPLOT to make a dot plot of two sequences in the Bioinformatics Toolbox 1.1.1 (R14SP1), I find the resulting plot difficult to interpret since there is no proper documentation on how the result was obtained. There appears to be more than one way in which such a plot can be made and I could not find anything in the documentation stating which of the many methods is used.

Answer 1

[MathWorks Support Team]

Documentation on the SEQDOTPLOT function in the Bioinformatics Toolbox 1.1.1 (R14SP1) is missing from the product and manual. At this point, we are looking into other ways of implementing sequence matching and updating the documentation related to the function. Here is some additional information on the SEQDOTPLOT function.

The SEQDOTPLOT function in the Bioinformatics Toolbox works as follows.

Start with two sequences:

x = AAAAAAA

y = AAATAAA

Execute the SEQDOTPLOT function in the following syntax.

seqdotplot(x,y,2,1);

In the above command, 2 is the window size and 1 is the number of characters within that window that match. In other words, the above command checks to see if there is at least one match within a window size of two. The way SEQDOTPLOT is implemented is that it checks if there is a match between the first characters within a window. If there is a match, then the corresponding matching square is blackened in the graph and the rest of the window is examined to check for a match. If the first characters does not match, then the window moves forward by one. This process continues until all window combinations have been exhausted. The reason for checking is to see if the first characters match has to do with the penalty associated in the way the matching is done.