Background on Nucleic Acid Dot Plots

Dot plots provide a simple, yet extremely powerful means of nucleic acid sequence analysis. Most commonly they are examined to identify one of two situations:

• Regions of similarity within a single molecule (i.e. repeats) or between different molecules.
• Sequences that have the potential for forming secondary structure by intramolecular base-pairing

The principle used to generate dot plots is straightforward. A matrix comparison of two sequences (or one with itself) is prepared by "sliding" a window of user-defined size along both sequences. If the two sequences within that window match with a precision set by the mismatch limit, a dot is placed in the middle of the window signifying a match.

In the following example, a mismatch limit of 2 means that up to 2 of 5 bases may mismatch and the 5 base window will still be classified as a match; when mismatch limit is set to 0, all 5 bases must match perfectly in order for the windows to match.

You can adjust the "stringency" of the match by adjusting window size and mismatch limit - the large the window of comparison, and the lower the mismatch limit, the most stringent the comparison.

The image below shows the results of a dot plot of a retrovirus vector sequence against itself using a window size of 9 and mismatch limit of 2. The sequence has nearly identical long terminal repeats at each end (red) and within the LTRs are a pair of nearly identical enhancer seqeunces (yellow).

Notice the patterns on either side of the main diagnonals that are generated by these repetitive regions. Notice also the random scattering of dots reflecting small regions that match fairly closely by chance. Most of these would disappear if the mismatch limit was set lower or the window size higher.

References

• Maizel JV and Lenk RP: Enhanced graphic matrix analysis of nucleic acid and protein sequences. Proc Natl Acad Sci USA 78:7665, 1981.
• Pustell J and Kafatos FC: A high speed, high capacity homology matrix: Zooming through SV40 and polyoma. Nucleic Acids Res 10:4765, 1982.
• Quigley GJ, Gehrke L, Roth DA and Auron PE: Computer-aided nucleic acid secondary structure modeling incorporating enzymatic digestion data. Nucleic Acids Res 12:347, 1984.