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A Fast Algorithm for Large Common Connected Induced Subgraphs

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Algorithms for Computational Biology (AlCoB 2017)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 10252))

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Abstract

We present a fast algorithm for finding large common subgraphs, which can be exploited for detecting structural and functional relationships between biological macromolecules. Many fast algorithms exist for finding a single maximum common subgraph. We show with an example that this gives limited information, motivating the less studied problem of finding many large common subgraphs covering different areas. As the latter is also hard, we give heuristics that improve performance by several orders of magnitude. As a case study, we validate our findings experimentally on protein graphs with thousands of atoms.

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Acknowledgments

Work partially supported by projects MIUR PRIN 2012C4E3KT (all authors except LT, LV) and UNIPI PRA_2015_0058 (authors RG, LT).

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Authors and Affiliations

  1. Inria, Università di Pisa and Erable, Pisa, Italy

    Alessio Conte, Roberto Grossi & Andrea Marino

  2. IRCAN, CNRS UMR, 7284, Nice, France

    Lorenzo Tattini

  3. Scuola Normale Superiore, Pisa, Italy

    Luca Versari

Authors
  1. Alessio Conte
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  2. Roberto Grossi
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  3. Andrea Marino
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  4. Lorenzo Tattini
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  5. Luca Versari
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Corresponding author

Correspondence to Andrea Marino .

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Editors and Affiliations

  1. University of Aveiro, Aveiro, Portugal

    Daniel Figueiredo

  2. Rovira i Virgili University, Tarragona, Spain

    Carlos Martín-Vide

  3. University of Aveiro, Aveiro, Portugal

    Diogo Pratas

  4. University of Extremadura, Caceres, Spain

    Miguel A. Vega-Rodríguez

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Conte, A., Grossi, R., Marino, A., Tattini, L., Versari, L. (2017). A Fast Algorithm for Large Common Connected Induced Subgraphs. In: Figueiredo, D., Martín-Vide, C., Pratas, D., Vega-Rodríguez, M. (eds) Algorithms for Computational Biology. AlCoB 2017. Lecture Notes in Computer Science(), vol 10252. Springer, Cham. https://doi.org/10.1007/978-3-319-58163-7_4

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  • DOI: https://doi.org/10.1007/978-3-319-58163-7_4

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-58162-0

  • Online ISBN: 978-3-319-58163-7

  • eBook Packages: Computer ScienceComputer Science (R0)

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