Algorithms for RH Mapping: New Ideas and Improved Analysis

Lars Ivansson, Jens Lagergren

Abstract: Radiation hybrid (RH) mapping is a technique for constructing a physical map describing the locations of n markers on a chromosome of an organism. In [J. Comput. Biol., 4 (1997), pp. 517--533], Ben-Dor and Chor presented new algorithms for the RH problem and gave the first performance guarantees for such algorithms. We improve the lower bounds on the number of experiments in a way that is sufficient for two of these algorithms to give a correct ordering of the markers with high probability. Not only are the new bounds tighter, but our analysis also captures to a much higher extent how the bounds depend on the actual arrangement of the markers. Furthermore, we modify the two algorithms to utilize RH mapping data produced with several radiation intensities. We show that the new algorithms are almost insensitive to the problem of using the correct intensity.