A new distance for high level RNA secondary structure comparison

Julien Allali 1 Marie-France Sagot 2, 3, 4
2 HELIX - Computer science and genomics
Inria Grenoble - Rhône-Alpes, LBBE - Laboratoire de Biométrie et Biologie Evolutive - UMR 5558
3 Baobab
PEGASE - Département PEGASE [LBBE]
Abstract : We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two new operations, called node fusion and edge fusion, besides the tree edit operations of deletion, insertion, and relabeling 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.
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  • HAL Id : hal-00306658, version 1
  • ARXIV : 0810.4002

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Julien Allali, Marie-France Sagot. A new distance for high level RNA secondary structure comparison. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Institute of Electrical and Electronics Engineers, 2005, 2, pp.3--14. ⟨hal-00306658⟩

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