Beyond Islands: Runs in Clone-Probe Matrices

David B. Wilson, David S. Greenberg, and Cynthia A. Phillips

Physical mapping is a fundamental component of the human genome project. A physical map consists of a set of probes which mark unique positions on a long fragment of DNA, together with the relative order of the probes on the DNA. This order is inferred from clone-probe hybridization experiments, which determine the probes contained within various fragments of the genome. In practice, the order of the probes is not completely determined by the hybridization experiments. To better design these experiments, researchers have analyzed the expected distribution of ``islands'' --- groups of probes which are known to be near one another --- that would result from hybridization experiments with different numbers of clones and probes. In this paper we analyze the distribution of ``runs'' --- groups of probes whose relative order is completely determined by the hybridization experiment. We include analytic, numerical, Monte Carlo, and simulation results on runs, which can further assist in the design of these experiments.

RECOMB 97, Proceedings of the First Annual International Conference on Computational Molecular Biology, pp. 320-329, 1997.
DVI version
GZipped PostScript version
conference slides

Scanned version in the ACM's Digital Library