JaMBW Chapter 3.2.1

Word Comparison


The following applet allows to compare sequences using the word matching mechanism well known as "DOT PLOT". Just paste in the horizontal sequence one sequence and in the vertical sequence a different one, fill in the word size and the step size and press compute. A set of dots will appear, identifying identical elements of the given size in the two sequences.

If instead you want to just analyze a single sequence, paste it in the horizontal sequence window and after having filled the word size and step size push compute. The dots will show the repeats present in your sequence, of that given size.


The "word comparison" is a conceptually very simple analysis which could produce very useful and deep insights. It can be used for analyse both single sequences and pair of sequences:

Some experiments useful to appreciate the value of the word matching algorithm


This applet accept at startup the following parameters: Planned improvements:
  1. allow a pure GIF or XBM output
  2. zooming
  3. ... anything else missing ? let me know !

Last modified:12 October 1996, by Luca I.G. TOLDO