Average complexity of the Jiang-Wang-Zhang pairwise tree alignment algorithm and of a RNA secondary structure alignment algorithm

Claire Herrbach 1 Alain Denise 2, 3, * Serge Dulucq 4
* Corresponding author
1 IGM - Institut de génétique et microbiologie [Orsay]
2 AMIB - Algorithms and Models for Integrative Biology
LIX - Laboratoire d'informatique de l'École polytechnique [Palaiseau], LRI - Laboratoire de Recherche en Informatique, UP11 - Université Paris-Sud - Paris 11, Inria Saclay - Ile de France
3 LRI - Laboratoire de Recherche en Informatique
4 LaBRI - Laboratoire Bordelais de Recherche en Informatique
Abstract : We prove that the average complexity of the pairwise ordered tree alignment algo- rithm of Jiang, Wang and Zhang is in O(nm), where n and m stand for the sizes of the two trees, respectively. We show that the same result holds for the aver- age complexity of pairwise comparison of RNA secondary structures, using a set of biologically relevant operations.
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Claire Herrbach, Alain Denise, Serge Dulucq. Average complexity of the Jiang-Wang-Zhang pairwise tree alignment algorithm and of a RNA secondary structure alignment algorithm. Theoretical Computer Science, Elsevier, 2010, 411, pp.2423-2432. ⟨inria-00541269⟩

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