COVERAGE PROCESSES IN PHYSICAL MAPPING BY ANCHORING RANDOM CLONES

The aim of this paper is to provide general results for predicting pro gress in a physical mapping project by anchoring random clones, when c lones and anchors are not homogeneously distributed along the genome, A complete physical map of the DNA of an organism consists of overlapp ing clones spanning the entire genome, Several schemes can be used to construct such a map, depending on the way that clones overlap, We foc us here on the approach consisting of assembling clones sharing a comm on random short sequence called an anchor, Some mathematical analyses providing statistical properties of anchored clones have been develope d in the stationary case, Modeling the clone and anchor processes as n onhomogeneous Poisson processes provides such an analysis in a general nonstationary framework, We apply our results to two natural nonhomog eneous models to illustrate the effect of inhomogeneity, This study re veals that using homogeneous processes for clones and anchors provides an overly optimistic assessment of the progress of the mapping projec t.