A Uniform Framework for Ordered Restriction Map Problems

Optical Mapping is an emerging technology for constructing ordered restriction maps of DNA molecules [1, 2, 3]. The underlying computational problems for this technology have been studied and several cost functions have been proposed in recent literature. Most of these propose combinatorial models; one of them also presents a probabilistic approach. However, it is not a priori clear as to how these cost functions relate to one another and to the underlying problem. We present a uniform framework for the restriction map problems where each of these various models is a specific instance of the basic framework. We achieve this by identifying the following approaches to the ordered restriction map problem: (1) using data consensus or agreement, and, (2) optimizing a characteristic function of the data. Our framework also opens up the possibility of exploring other cost functions. An additional feature is that we not only integrate the combinatorial models but also analyze the pro..