Bioinformatics pp 395-421 | Cite as

Developing Fixed-Parameter Algorithms to Solve Combinatorially Explosive Biological Problems

  • Falk Hüffner
  • Rolf Niedermeier
  • Sebastian Wernicke
Protocol
Part of the Methods in Molecular Biology™ book series (MIMB, volume 453)

Abstract

Fixed-parameter algorithms can efficiently find optimal solutions to some computationally hard (NP-hard) problems. This chapter surveys five main practical techniques to develop such algorithms. Each technique is circumstantiated by case studies of applications to biological problems. It also presents other known bioinformatics-related applications and gives pointers to experimental results.

Key words:

Computationally hard problems combinatorial explosions discrete problems fixed-parameter tractability optimal solutions 
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Notes

Acknowledgments

This work was supported by the Deutsche Forschungsgemein-schaft, Emmy Noether research group PIAF (fixed-parameter algorithms), NI 369/4 (Falk Hüffner), and the Deutsche Telekom Stiftung (Sebastian Wernicke).

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Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Falk Hüffner
    • 1
  • Rolf Niedermeier
    • 1
  • Sebastian Wernicke
    • 1
  1. 1.Institut für InformatikFriedrich-Schiller-Universität JenaJenaGermany

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