Motivation

Physical mapping is the process of determining the relative position of landmarks along a genome segment. The resulting maps are used as a basis for DNA sequencing, and for the isolation and characterization of individual genes or other DNA regions of interest (e.g., transcribed regions or regulatory elements). The construction of high resolution sequence-ready physical maps for human and other organisms is still one of the top priority tasks of the Human Genome Project. Given a long DNA segment it is relatively easy to produce a large group of DNA fragments known as clones. The process of creating the clones consists of breaking several copies of the original DNA sequence at many locations, and then cloning each of the fragments. One of the problems with the cloning process is that the resulting fragments are obtained "out of order". This means that it is difficult to re-assemble the fragments in order to get a map of the original sequence. Moreover, the cloning process does not ensure that a continuous sequence of DNA can be reconstructed from the fragments.