The generation of experimental fingerprints is the bottleneck of the procedure as described here. Once the fingerprints are generated for a certain species they can be rapidly applied in all possible settings. Therefore, we are developing improvements of this step. In addition, the use of a now available fifth fluorescent dye as a size marker in sequencing lanes should allow for a fast correlation between restriction fragment sizes (derived from the sequence) and gel run behaviors of DNA fragments (relative to the size marker). The latter improvement could not only lead to a faster generation of experimental fingerprints, but could also supply a large dataset to improve the prediction of gel run behaviors of fragments based on the sequence composition.