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Minimizing sets of enzymes to differentiate between species

A large number of species cannot be distinguished via standard non genetic analysis in the lab. In this paper we address the problem of finding minimum sets of restriction enzymes that can be used to unequivocally identify the species of a yeast specimen by analyzing the size of digested DNA fragments in gel electrophoresis experiments. The problem is first mapped into set covering and then solved using Constraint Programming techniques. Although the data sets used are relatively small (23 yeast species and 331 enzymes), a similar approach might be applicable to larger ones and to a number of variants as discussed in the conclusion. The subject of this paper has already raised the interest of our biologist partners and may become a benchmark for the application of Constraint Programming techniques to Bioinformatics.