How to Compare Arc-Annotated Sequences: The Alignment Hierarchy

  • Guillaume Blin
  • Hélène Touzet
Conference paper

DOI: 10.1007/11880561_24

Volume 4209 of the book series Lecture Notes in Computer Science (LNCS)
Cite this paper as:
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


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.


computational biology RNA structures arc-annotated sequences NP-hardness edit distance algorithm 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Guillaume Blin
    • 1
  • Hélène Touzet
    • 2
  1. 1.IGM-LabInfo – UMR CNRS 8049 – Université de Marne-la-ValléeMarne-la-ValléeFrance
  2. 2.LIFL – UMR CNRS 8022 – Université Lille 1Villeneuve d’AscqFrance