An algorithm combining discrete and continuous methods for optical mapping.

R M Karp; I Pe'er; R Shamir

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PubMed · 10786298

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 non-uniform discretization of the data. We present encouraging results on real experimental data.

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Algorithms Likelihood Functions Microscopy, Fluorescence Models, Statistical Probability Restriction Mapping Journal Article Research Support, Non-U.S. Gov't

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R M Karp, I Pe'er, R Shamir. 1999. An algorithm combining discrete and continuous methods for optical mapping.. https://pubmed.ncbi.nlm.nih.gov/10786298/

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