An Efficient Algorithm for Developing Topological Valid Matchings

We examine a problem that arises in physical DNA mapping, namely determining what common DNA is represented in two maps. We first present an example illustrating the properties of DNA mapping, and present some biological background supporting our approach. We present a new graph structure, called the \(\mathcal{Z}\)-graph, that takes advantage of structure that develops during the mapping process, thus catalyzing the discovery of all maximum, topologically valid matchings. We describe an algorithm based on this structure and present experimental data supporting its improved performance as compared with a naive approach.