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Segmentation with an Isochore Distribution

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Algorithms in Bioinformatics (WABI 2006)

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

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Abstract

We introduce a novel generative probabilistic model for segmentation problems in molecular sequence analysis. All segmentations that satisfy given minimum segment length requirements are equally likely in the model. We show how segmentation-related problems can be solved with similar efficacy as in hidden Markov models. In particular, we show how the best segmentation, as well as posterior segment class probabilities in individual sequence positions can be computed in O(nC) time in case of C segment classes and a sequence of length n.

Work supported by a grant from the Natural Sciences and Engineering Research Council of Canada.

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Author information

Authors and Affiliations

  1. Department of Computer Science and Operations Research, Université de Montréal, C.P. 6128, succ. Centre-Ville, Montréal, Québec, H3C 3J7, Canada

    Miklós Csűrös, Ming-Te Cheng & Amine Halawani

  2. Lehr- und Forschungseinheit für Bioinformatik, Ludwig-Maximilians-Universität München, 80333, München, Germany

    Andreas Grimm

  3. Institut Scientifique Polytechnique Galilée, Université Paris XIII, 93430, Villetaneuse, France

    Perrine Landreau

Authors
  1. Miklós Csűrös
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  2. Ming-Te Cheng
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  3. Andreas Grimm
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  4. Amine Halawani
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  5. Perrine Landreau
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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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Csűrös, M., Cheng, MT., Grimm, A., Halawani, A., Landreau, P. (2006). Segmentation with an Isochore Distribution. 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_36

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  • DOI: https://doi.org/10.1007/11851561_36

  • 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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