How to compare arc-annotated sequences: the alignment hierarchy

Authors:
Guillaume Blin;Hélène Touzet
Affiliations:
IGM-LabInfo – UMR CNRS 8049 – Université de Marne-la-Vallée, Marne-la-Vallée, France;LIFL – UMR CNRS 8022 – Université Lille 1, Villeneuve d’Ascq, France
Venue:
SPIRE'06 Proceedings of the 13th international conference on String Processing and Information Retrieval
Year:
2006

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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.