An algorithm combining discrete and continuous methods for optical mapping

R. M. Karp*, I. Pe'er, R. Shamir

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


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.

Original languageEnglish
Pages (from-to)745-760
Number of pages16
JournalJournal of Computational Biology
Issue number5
StatePublished - 2000


  • Discrete optimization
  • EM algorithm
  • Maximum likelihood
  • Optical mapping
  • Restriction maps


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