Simple fast algorithms for the editing distance between trees and related problems
SIAM Journal on Computing
The Tree-to-Tree Correction Problem
Journal of the ACM (JACM)
Alignment of Trees - An Alternative to Tree Edit
CPM '94 Proceedings of the 5th Annual Symposium on Combinatorial Pattern Matching
Local Similarity in RNA Secondary Structures
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Pure Multiple RNA Secondary Structure Alignments: A Progressive Profile Approach
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Towards a Weighted-Tree Similarity Algorithm for RNA Secondary Structure Comparison
HPCASIA '05 Proceedings of the Eighth International Conference on High-Performance Computing in Asia-Pacific Region
A heuristic algorithm for clustering rooted ordered trees
Intelligent Data Analysis
A multiple layer model to compare RNA secondary structures
Software—Practice & Experience
Stability of RNA structural motifs and its influence on editing efficiency by adenosine deaminases
International Journal of Bioinformatics Research and Applications
Finding common RNA pseudoknot structures in polynomial time
Journal of Discrete Algorithms
Finding common RNA pseudoknot structures in polynomial time
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
Local alignment of RNA sequences with arbitrary scoring schemes
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
An edit distance between RNA stem-loops
SPIRE'05 Proceedings of the 12th international conference on String Processing and Information Retrieval
A multiple graph layers model with application to RNA secondary structures comparison
SPIRE'05 Proceedings of the 12th international conference on String Processing and Information Retrieval
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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.