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

Authors:
Claire Herrbach;Alain Denise;Serge Dulucq
Affiliations:
LRI, Université/ Paris-Sud 11, CNRS, Bâ/t. 490, 91405 Orsay Cedex, France and IGM, Université/ Paris-Sud 11, CNRS/ Bâ/t. 400/ 91405 Orsay Cedex, France;LRI, Université/ Paris-Sud 11, CNRS, Bâ/t. 490, 91405 Orsay Cedex, France and IGM, Université/ Paris-Sud 11, CNRS/ Bâ/t. 400/ 91405 Orsay Cedex, France;LaBRI, Université/ Bordeaux 1, CNRS, 33405 Talence Cedex, France
Venue:
Theoretical Computer Science
Year:
2010

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Abstract

We prove that the average complexity of the pairwise ordered tree alignment algorithm 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 average complexity of pairwise comparison of RNA secondary structures, using a set of biologically relevant operations.