Algorithms for optical mapping

Richard M. Karp, Ron Shamir

Research output: Contribution to conferencePaperpeer-review

Abstract

Optical mapping is a novel technique for determining the restriction sites on a DNA molecule by directly observing a number of partially digested copies of the molecule under a light microscope. The problem is complicated by uncertainty as to the orientation of the molecules and by erroneous detection of cuts. In this paper we study the problem of constructing a restriction map based on optical mapping data. We give several variants of a polynomial-time reconstruction algorithm, as well as an algorithm that is exponential in the number of cut sites, and hence is appropriate only for a small number of cut sites. We give a simple probabilistic model for data generation and for the errors and prove probabilistic upper and lower bounds on the number of molecules needed by each algorithm in order to obtain a correct map, expressed as a function of the number of cut sites and the error parameters. To the best of our knowledge, this is the first probabilistic analysis of algorithms for the problem. We also provide experimental results confirming that our algorithms are highly effective on simulated data.

Original languageEnglish
Pages117-124
Number of pages8
DOIs
StatePublished - 1998
Externally publishedYes
EventProceedings of the 1998 2nd Annual International Conference on Computational Molecular Biology - New York, NY, USA
Duration: 22 Mar 199825 Mar 1998

Conference

ConferenceProceedings of the 1998 2nd Annual International Conference on Computational Molecular Biology
CityNew York, NY, USA
Period22/03/9825/03/98

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