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Superbubbles as an empirical characteristic of directed networks

Published online by Cambridge University Press:  01 September 2020

Fabian Gärtner ,
Felix Kühnl Open the ORCID record for Felix Kühnl [Opens in a new window] ,
Carsten R. Seemann Open the ORCID record for Carsten R. Seemann [Opens in a new window] ,
Christian Höner Zu Siederdissen Open the ORCID record for Christian Höner Zu Siederdissen [Opens in a new window] ,
Peter F. Stadler Open the ORCID record for Peter F. Stadler [Opens in a new window]  and
The Students of the Graphs and Networks Computer Lab 2018/19
Fabian Gärtner
Affiliation:
Competence Center for Scalable Data Services and Solutions Dresden/Leipzig (scaDS), Universität Leipzig, Augustusplatz 12, D-04107 Leipzig, Germany (e-mail: fabian@bioinf.uni-leipzig.de) Bioinformatics Group, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany (e-mails: carsten@bioinf.uni-leipzig.de, felix@bioinf.uni-leipzig.de, choener@bioinf.uni-leipzig.de)
Felix Kühnl
Affiliation:
Bioinformatics Group, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany (e-mails: carsten@bioinf.uni-leipzig.de, felix@bioinf.uni-leipzig.de, choener@bioinf.uni-leipzig.de) Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany
Carsten R. Seemann
Affiliation:
Bioinformatics Group, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany (e-mails: carsten@bioinf.uni-leipzig.de, felix@bioinf.uni-leipzig.de, choener@bioinf.uni-leipzig.de) Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany
Christian Höner Zu Siederdissen
Affiliation:
Bioinformatics Group, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany (e-mails: carsten@bioinf.uni-leipzig.de, felix@bioinf.uni-leipzig.de, choener@bioinf.uni-leipzig.de) Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany
Peter F. Stadler*
Affiliation:
Competence Center for Scalable Data Services and Solutions Dresden/Leipzig (scaDS), Universität Leipzig, Augustusplatz 12, D-04107 Leipzig, Germany (e-mail: fabian@bioinf.uni-leipzig.de) Bioinformatics Group, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany (e-mails: carsten@bioinf.uni-leipzig.de, felix@bioinf.uni-leipzig.de, choener@bioinf.uni-leipzig.de) Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Universität Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany Leipzig Research Center for Civilization Diseases, Universität Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany Institute for Theoretical Chemistry, University of Vienna, Währingerstraße17, A-1090 Wien, Austria Facultad de Ciencias, Universidad National de Colombia, Sede Bogotá, Colombia Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM87501, USA
The Students of the Graphs and Networks Computer Lab 2018/19
Affiliation:
Bioinformatics Group, Department of Computer Science, Universität Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany (e-mails: carsten@bioinf.uni-leipzig.de, felix@bioinf.uni-leipzig.de, choener@bioinf.uni-leipzig.de)
*
*Corresponding author. Email: studla@bioinf.uni-leipzig.de
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Abstract

Superbubbles are acyclic induced subgraphs of a digraph with single entrance and exit that naturally arise in the context of genome assembly and the analysis of genome alignments in computational biology. These structures can be computed in linear time and are confined to non-symmetric digraphs. We demonstrate empirically that graph parameters derived from superbubbles provide a convenient means of distinguishing different classes of real-world graphical models, while being largely unrelated to simple, commonly used parameters.

Keywords

digraphgraph descriptorbubbleslinear time algorithm
Type
Research Article
Information
Network Science , Volume 9 , Issue 1 , March 2021 , pp. 49 - 58
Copyright
© The Author(s), 2020. Published by Cambridge University Press

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Footnotes

Action Editor: Ulrik Brandes

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