An edit distance between RNA stem-loops

Authors:
Valentin Guignon;Cedric Chauve;Sylvie Hamel
Affiliations:
Programme de Bioinformatique, Université de Montréal, Montréal, (QC), Canada;LaCIM, Département d'Informatique, Université du Québec à Montréal, Montréal, (QC), Canada;LBIT, DIRO, Université de Montréal, Montréal, (QC), Canada
Venue:
SPIRE'05 Proceedings of the 12th international conference on String Processing and Information Retrieval
Year:
2005

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Abstract

We introduce the notion of conservative edit distance and mapping between two RNA stem-loops. We show that unlike the general edit distance between RNA secondary structures, the conservative edit distance can be computed in polynomial time and space, and we describe an algorithm for this problem. We show how this algorithm can be used in the more general problem of complete RNA secondary structures comparison.