The detection of atypical regions is based on the observation of deviation of local signatures (i.e. signature of small fragments of DNA) from the genomic signature of the recipient species. Genomes are consequently sampled by means of a sliding window with an appropriate size. In fact, it would be interesting to have windows the smallest as possible for highest sampling accuracy. However, intra-genomic variability of signature increases for small windows. In addition, variability depends on species and word length. Base composition (1-letter word), 2-and 3-letter words are poorly speciesspecific: they do not allow a good discrimination between species (25, 27) . As a general rule, the longer the words (up to 9-letter long), the higher the specificity of the signature (25, 27, 31) . However, counts of long words in small windows are too low to allow a reliable estimation of the parameters. In our hands, the analysis of 4-letter words in a sliding window of 5 kb (with a 0.5 kb step) offers a good trade-off between reliability of count, file size and computational charge, whatever the species. In addition, a double-strand signature (called local signature thereafter) is computed for each window to get rid of variations induced by strand asymmetry (38) (39) (40) (41) (42) .