Use dot plots to quickly confirm similarity between two sequences

We occasionally get e-mails from users who think that two sequences should align using ClustalW or the Align To Reference function, but the algorithms cannot find any meaningful matches. In these cases, the first thing I do is open both sequences and then create a dot-plot between them using the Analyze | Create Dotplot | Pustell DNA Matrix function. There is also a protein version and even a DNA versus Protein version. This is a great tool for getting a quick overview of the sequence similarity between a pair of sequences.


A – The two sequences are essentially identical and in the same orientation. The diagonal runs from top left to bottom right and is drawn in black. You also see this pattern if you test a sequence against itself.

B – The two sequences are essentially identical, but one is “flipped” relative to the other so you see a full-length diagonal running bottom left to top right in blue.

C – One of the sequences has a section in the middle that is inverted relative to the other.

D – The two sequences are similar, but are far from identical, resulting in a dotted line.

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