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Fully Dynamic de Bruijn Graphs

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String Processing and Information Retrieval (SPIRE 2016)

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Abstract

We present a space- and time-efficient fully dynamic implementation of de Bruijn graphs, which can also support fixed-length jumbled pattern matching.

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Notes

  1. 1.

    An alternative definition, which our data structure can be made to handle but which we do not consider in this paper, has an edge from u to v whenever both nodes are in the graph.

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Acknowledgements

Many thanks to Rayan Chikhi and the anonymous reviewers for their comments.

Author information

Authors and Affiliations

  1. CERIST, Ben Aknoun, Algiers, Algeria

    Djamal Belazzougui

  2. Helsinki Institute for Information Technology, Helsinki, Finland

    Travis Gagie & Veli Mäkinen

  3. University of Helsinki, Helsinki, Finland

    Travis Gagie & Veli Mäkinen

  4. University of Milano-Bicocca, Milan, Italy

    Marco Previtali

Authors
  1. Djamal Belazzougui
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  2. Travis Gagie
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  3. Veli Mäkinen
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  4. Marco Previtali
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Corresponding author

Correspondence to Travis Gagie .

Editor information

Editors and Affiliations

  1. Kyushu University , Fukuoka, Japan

    Shunsuke Inenaga

  2. Mathematical Informatics, University of Tokyo , Tokyo, Japan

    Kunihiko Sadakane

  3. Computer Science, Waseda University , Tokyo, Japan

    Tetsuya Sakai

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Belazzougui, D., Gagie, T., Mäkinen, V., Previtali, M. (2016). Fully Dynamic de Bruijn Graphs. In: Inenaga, S., Sadakane, K., Sakai, T. (eds) String Processing and Information Retrieval. SPIRE 2016. Lecture Notes in Computer Science(), vol 9954. Springer, Cham. https://doi.org/10.1007/978-3-319-46049-9_14

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  • DOI: https://doi.org/10.1007/978-3-319-46049-9_14

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  • Print ISBN: 978-3-319-46048-2

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