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How to Compare Arc-Annotated Sequences: The Alignment Hierarchy

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String Processing and Information Retrieval (SPIRE 2006)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 4209))

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Abstract

We describe a new unifying framework to express comparison of arc-annotated sequences, which we call alignment of arc-annotated sequences. We first prove that this framework encompasses main existing models, which allows us to deduce complexity results for several cases from the literature. We also show that this framework gives rise to new relevant problems that have not been studied yet. We provide a thorough analysis of these novel cases by proposing two polynomial time algorithms and an NP-completeness proof. This leads to an almost exhaustive study of alignment of arc-annotated sequences.

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Author information

Authors and Affiliations

  1. IGM-LabInfo – UMR CNRS 8049 – Université de Marne-la-Vallée, 77 454 Cedex 2, Marne-la-Vallée, France

    Guillaume Blin

  2. LIFL – UMR CNRS 8022 – Université Lille 1, 59 655 Cedex, Villeneuve d’Ascq, France

    Hélène Touzet

Authors
  1. Guillaume Blin
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  2. Hélène Touzet
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Editor information

Editors and Affiliations

  1. Department of Computer and Information Science, University of Strathclyde, Scotland

    Fabio Crestani

  2. Dipartimento di Informatica, University of Pisa, Largo B. Pontecorvo 3, 56127, Pisa, Italy

    Paolo Ferragina

  3. Department of Information Studies, University of Sheffield, Sheffield, UK

    Mark Sanderson

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© 2006 Springer-Verlag Berlin Heidelberg

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Blin, G., Touzet, H. (2006). How to Compare Arc-Annotated Sequences: The Alignment Hierarchy. In: Crestani, F., Ferragina, P., Sanderson, M. (eds) String Processing and Information Retrieval. SPIRE 2006. Lecture Notes in Computer Science, vol 4209. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11880561_24

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  • DOI: https://doi.org/10.1007/11880561_24

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-45774-9

  • Online ISBN: 978-3-540-45775-6

  • eBook Packages: Computer ScienceComputer Science (R0)

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