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PubMed · 11153097

An algorithm combining discrete and continuous methods for optical mapping.

R M Karp·I Pe'er·R Shamir
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Abstract

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 fluorescence 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 nonuniform discretization of the data. We present encouraging results on real experimental data and on simulated data.

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AlgorithmsComputer SimulationDNAMicroscopy, FluorescenceOptics and PhotonicsRestriction MappingJournal Article

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R M Karp, I Pe'er, R Shamir. 2000. An algorithm combining discrete and continuous methods for optical mapping.. https://doi.org/10.1089/106652701446189

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