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International Workshop on Algorithms in Bioinformatics

WABI 2006: Algorithms in Bioinformatics pp 298–309Cite as

Integer Linear Programs for Discovering Approximate Gene Clusters

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Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 4175))

Abstract

We contribute to the discussion about the concept of approximate conserved gene clusters by presenting a class of definitions that (1) can be written as integer linear programs (ILPs) and (2) allow several variations that include existing definitions such as common intervals, r-windows, and max-gap clusters or gene teams. While the ILP formulation does not directly lead to optimal algorithms, it provides unprecedented generality and is competitive in practice for those cases where efficient algorithms are known. It allows for the first time a non-heuristic study of large approximate clusters in several genomes. Source code and datasets are available at http://gi.cebitec.uni-bielefeld.de/assb .

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Author information

Authors and Affiliations

  1. Algorithms and Statistics for Systems Biology group, Genome Informatics, Technische Fakultät, Bielefeld University, D-33594, Bielefeld, Germany

    Sven Rahmann

  2. International NRW Graduate School in Bioinformatics and Genome Research,  

    Sven Rahmann

  3. Mathematics in Life Sciences group, Dept. of Mathematics and Computer Science, Free University Berlin, D-14195, Berlin, Germany

    Gunnar W. Klau

  4. DFG Research Center Matheon “Mathematics for key technologies”, Berlin

    Gunnar W. Klau

Authors
  1. Sven Rahmann
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  2. Gunnar W. Klau
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Editor information

Editors and Affiliations

  1. Ecole Polytechnique Fédérale de Lausanne, Switzerland

    Philipp Bücher

  2. Laboratory for Computational Biology and Bioinformatics, EPFL (Ecole Polytechnique Fédérale de Lausanne), Swiss Institute of Bioinformatics, Lausanne, Switzerland

    Bernard M. E. Moret

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© 2006 Springer-Verlag Berlin Heidelberg

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Rahmann, S., Klau, G.W. (2006). Integer Linear Programs for Discovering Approximate Gene Clusters. In: Bücher, P., Moret, B.M.E. (eds) Algorithms in Bioinformatics. WABI 2006. Lecture Notes in Computer Science(), vol 4175. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11851561_28

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  • DOI: https://doi.org/10.1007/11851561_28

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-39583-6

  • Online ISBN: 978-3-540-39584-3

  • eBook Packages: Computer ScienceComputer Science (R0)

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