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Algorithmica

, Volume 13, Issue 1–2, pp 52–76 | Cite as

Physical mapping of chromosomes: A combinatorial problem in molecular biology

  • F. Alizadeh
  • R. M. Karp
  • L. A. Newberg
  • D. K. Weisser
Article

Abstract

This paper is concerned wth the physical mapping of DNA molecules using data about the hybridization of oligonucleotide probes to a library of clones. In mathematical terms, the DNA molecule corresponds to an interval on the real line, each clone to a subinterval, and each probe occurs at a finite set of points within the interval. A stochastic model for the occurrences of the probes and the locations of the clones is assumed. Given a matrix of incidences between probes and clones, the task is to reconstruct the most likely interleaving of the clones. Combinatorial algorithms are presented for solving approximations to this problem, and computational results are presented.

Key words

Clone DNA Local search Maximum likelihood Oligonucleotide Physical mapping Probe Traveling-salesman problem 

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Copyright information

© Springer-Verlag New York Inc. 1995

Authors and Affiliations

  • F. Alizadeh
    • 1
  • R. M. Karp
    • 1
    • 2
  • L. A. Newberg
    • 2
  • D. K. Weisser
    • 2
  1. 1.International Computer Science InstituteBerkeleyUSA
  2. 2.Computer Science DivisionUniversity of CaliforniaBerkeleyUSA

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