Novel tree edit operations for RNA secondary structure comparison

Julien Allali (1) , Marie-France Sagot (2, 3, 4)

1 LIGM - Laboratoire d'Informatique Gaspard-Monge
2 HELIX - Computer science and genomics
3 DCS - Department of Computer Science
4 Baobab

We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two novel operations, called node fusion and edge fusion, besides the tree edit operations of deletion, insertion and relabelling classically used in the literature. This allows us to address some serious limitations of the more traditional tree edit operations when the trees represent RNAs and what is searched for is a common structural core of two RNAs. Although the algorithm complexity has an exponential term, this term depends only on the number of successive fusions that may be applied to a same node, not on the total number of fusions. The algorithm remains therefore efficient in practice and is used for illustrative purposes on ribosomal as well as on other types of RNAs.

Mots clés: distance; RNA; secondary structure; tree comparison; edit operation

Domaines: Autre [cs.OH]; Algorithme et structure de données [cs.DS]

Julien Allali, Marie-France Sagot. Novel tree edit operations for RNA secondary structure comparison. Workshop on Algorithms in Bioinformatics 2004, 2004, Bergen, Denmark. pp.412--425, ⟨10.1007/978-3-540-30219-3_35⟩. ⟨hal-00306661⟩