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Optimization Problems in Molecular Biology

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Advances in Optimization and Approximation

Part of the book series: Nonconvex Optimization and Its Applications ((NOIA,volume 1))

Abstract

Molecular biology has raised many interesting and deep mathematical and computational questions. For example, given the DNA or protein sequences of several organisms, can we know how much they are related to each other by computing an optimal alignment or, in particular, a longest common subsequence, of the sequences? Is it possible to reconstruct the evolutionary process for a set of extant species from their DNA sequences? Given many small overlapping fragments of a DNA molecule, how do we recover the DNA sequence? Will the shortest common superstring of these fragments give a good estimate? How many fragments suffice to guarantee that the reconstructed sequence is within 99% of the true DNA sequence? An organism can evolve by chromosome inversions, and this raises the question of how to transform one sequence into another with the smallest number of reversals.

Rather than an extensive literature survey, the purpose of this article is to introduce in depth several prominent optimization problems arising in molecular biology. We will emphasize recent developments and provide proof sketches for the results whenever possible.

ArticleNote

Supported in part by NSERC Operating Grant OGP0046613.

Supported in part by NSERC Operating Grant OGP0046506.

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Author information

Authors and Affiliations

  1. Department of Computer Science and Systems, McMaster University, Hamilton, Ont., L8S 4K1, Canada

    Tao Jiang

  2. Department of Computer Science, University of Waterloo, Waterloo, Ont, N3L 3G1, Canada

    Ming Li

Authors
  1. Tao Jiang
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  2. Ming Li
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Editor information

Editors and Affiliations

  1. University of Minnesota, USA

    Ding-Zhu Du

  2. Institute of Applied Mathematics, Beijing, China

    Ding-Zhu Du

  3. National University of Singapore, Singapore

    Jie Sun

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© 1994 Kluwer Academic Publishers

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Jiang, T., Li, M. (1994). Optimization Problems in Molecular Biology. In: Du, DZ., Sun, J. (eds) Advances in Optimization and Approximation. Nonconvex Optimization and Its Applications, vol 1. Springer, Boston, MA. https://doi.org/10.1007/978-1-4613-3629-7_10

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  • DOI: https://doi.org/10.1007/978-1-4613-3629-7_10

  • Publisher Name: Springer, Boston, MA

  • Print ISBN: 978-1-4613-3631-0

  • Online ISBN: 978-1-4613-3629-7

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