Beyond Islands: Runs in Clone-Probe Matrices
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.
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