Molecular Toolkit Index Toolkit Help

Nucleic Acid Dot Plots

Dot or matrix plots provide an easy and powerful means of sequence analysis, useful for searching out regions of similarity in two sequences and repeats within a single sequence. Background information on generating and and interpreting dot plots is available.

The program requires two nucleic acid sequences, which can be pasted into the text boxes labeled DNA Number 1 and DNA Number 2. The two sequences can be, and often are, identical. RNA sequences can also be entered; U's are automatically converted to T's. Two options are available for loading of the two sequences:

  • Click Demo DNA -> DNA1 button to retrieve a demonstration sequence and inserts it into the DNA 1 text box.
  • Click Copy DNA1 -> DNA2 button to copy the sequence in the DNA 1 text box to the DNA 2 text box. This is useful for setting up to compare a sequence to itself and search for repeated regions.

Two user-defined parameters can be set to control production of the matrix:

  • Window Size is number of bases in a sliding window that is moved along each sequence and compared to generate a single data point on the plot. Window size must be an odd number.
  • Mismatch Limit determines how similar the two sequences in a window must be to "match". For example, if window size is 9 and mismatch limit is 2, then up to 2 mismatches in a 9 base window will still be classified as a match.

After filling each text box with a sequence and setting window size and mismatch limit, click the Plot button. Note that all messages, including error alerts, are displayed in the yellow text box.

Once a plot is generated, clicking on a point within it will generate a message describing the relative position (base number) in the two sequences.

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Last updated on June 24, 1998
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