570 Int. J. Bioinformatics Research and Applications, Vol. 5, No. 5, 2009 The Double Digest Problem: finding all solutions S. Sur-Kolay* Advanced Computing and Microelectronics Unit, Indian Statistical Institute, Kolkata 700108, India E-mail: ssk@isical.ac.in *Corresponding author S. Banerjee Computation and Communication Technologies Group, Honeywell Technology Solutions (HTS), Bangalore, India E-mail: Satyajit.Banerjee@honeywell.com S. Mukhopadhyaya Department of Computer Science and Engineering, Birla Institute of Technology, Mesra, Kolkata Campus, Kolkata 700107, India E-mail: smukhopadhyaya@bitmesra.ac.in C.A. Murthy Machine Intelligence Unit, Indian Statistical Institute, Kolkata 700108, India E-mail: murthy@isical.ac.in Abstract: The strongly NP-complete Double Digest Problem (DDP), for physical mapping of DNA, is now used for efficient genotyping. Existing methods: • are inefficient in tackling large instances • produce only one solution while an instance may have multiple distinct solutions. In this paper, we employ the notion of equivalence among the distinct solutions to obtain almost all of them. Our method comprises two phases: • finding a representative from each equivalence class using an elitist Genetic Algorithm (GA) • for each representative generating the entire class efficiently. Experimental results tally for known instances. Significant reduction in search space provides notable efficiency. Copyright © 2009 Inderscience Enterprises Ltd.