|Molecular Toolkit Index||Toolkit Help|
|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:
Two user-defined parameters can be set to control production of the matrix:
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.