Local matching of random restriction maps

Optical mapping is a new technique to generate restriction maps of DNA easily and quickly. DNA restriction maps can be aligned by comparing corresponding restriction fragment lengths. To relate, organize, and analyse these maps it is necessary to rapidly compare maps. The issue of the statistical significance of approximately matching maps then becomes central, as in BLAST with sequence scoring. In this paper, we study the approximation to the distribution of counts of matched regions of specified length when comparing two DNA restriction maps. Distributional results are given to enable us to compute p-values and hence to determine whether or not the two restriction maps are related. The key tool used is the Chen-Stein method of Poisson approximation. Certain open problems are described.