Genomics via Optical Mapping II: Ordered Restriction Maps

In this paper, we describe our algorithmic approach to constructing ordered restriction maps based on the data created from the images of population of individual DNA molecules (clones) digested by restriction enzymes. The goal is to devise map-making algorithms capable of producing high-resolution, high-accuracy maps rapidly and in a scalable manner. The resulting software is a key component of our optical mapping automation tools and has been used routinely to map cosmid, lambda and BAC clones. The experimental results appear highly promising.