An Algorithm Combining Discrete and Continuous Methods for Optical Mapping

Proceedings Of The Seventh International Conference On Intelligent Systems For Molecular Biology

Volume

Proceedings Of The Seventh International Conference On Intelligent Systems For Molecular Biology

Contents

Optical mapping is a novel technique for generating the restriction map of a DNA molecule by observing many single, partially digested, copies of it, using florescence microscopy. The real-life problem is complicated by numerous factors: false positive and false negative cut observations, inaccurate location measurements, unknown orientations and faulty molecules. We present an algorithm for solving the real-life problem. The algorithm combines continuous optimization and combinatorial algorithms, applied to a non-uniform discretization of the data. We present encouraging results on real experimental data.