Genosphere Project, ERATO JRDC.
The representation of sequence similarity by dot matrix plots is a widely used method for the comparing two biological sequences. it presents the user an over-all view of similarity between two sequences. We reconsider the computation of this plot. Improvement is proposed through the preprocessing of the sequence into a an automaton recognizing the word structure of a sequence. The main advantage of this approach is to eliminate systematically the repetitions during word comparison. As a result, large sequences can be handled more efficiently.