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String Selection Problems

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Optimization Approaches for Solving String Selection Problems

Part of the book series: SpringerBriefs in Optimization ((BRIEFSOPTI))

Abstract

The increasing amount of genomic data and the ability to synthesize artificial DNA constructs poses a series of challenging problems involving the identification and design of sequences with specific properties. We address the identification of such sequences; many of these problems present challenges both at biological and computational level. In this chapter, we introduce the main string selection problems and the theoretical and experimental results for the most important instances.

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Notes

  1. 1.

    Informally, the goal of parameterized complexity is to study how the different parameters of the input instance affect the running time of the algorithm.

  2. 2.

    ZPP is the Zero-error Probabilistic Polynomial Time complexity class. It is defined as the class of languages recognized by probabilistic Turing machine with polynomial bounded average run time and zero error probability [30].

  3. 3.

    APX is defined as the class of all NP-optimization problems P such that, for some r ≥ 1, there exists a polynomial time r-approximate algorithm for P [3].

  4. 4.

    FPT denotes the class of fixed-parameter tractable problems, which are problems that can be solved in time \(f(k)\vert x{\vert }^{\mathcal{O}(1)}\) for some computable function f.

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Authors and Affiliations

  1. Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA

    Elisa Pappalardo & Giovanni Stracquadanio

  2. Center for Applied Optimization Department of Industrial and Systems Engineering, University of Florida, Gainesville, FL, USA

    Panos M. Pardalos

  3. Laboratory of Algorithms and Technologies for Networks Analysis (LATNA) Higher School of Economics, National Research University, Moscow, Russia

    Panos M. Pardalos

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  1. Elisa Pappalardo
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  2. Panos M. Pardalos
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  3. Giovanni Stracquadanio
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© 2013 Elisa Pappalardo, Panos M. Pardalos, Giovanni Stracquadanio

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Pappalardo, E., Pardalos, P.M., Stracquadanio, G. (2013). String Selection Problems. In: Optimization Approaches for Solving String Selection Problems. SpringerBriefs in Optimization. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-9053-1_4

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