Zones of low entropy in genomic sequences.

We consider the problem of detecting regions having low entropy in DNA sequences, which is a particular case of searching for dos-DNA zones. The entropy is measured in linear time as the number of distinct segments occurring in the regions. As a consequence, we are able to determine regions containing a small number of repetitions of long segments or a large number of repetitions of short segments. The method provides an index on sequences that is applied to compare them without any alignment. Comparisons extract regions having similar combinatorial features that would not have been found by standard alignment methods. The present methodology is applied to Saccharomyces cerevisiae yeast chromosomes to show what the approach is able to produce.