Algorithms for approximate string matching
Information and Control
Simple fast algorithms for the editing distance between trees and related problems
SIAM Journal on Computing
Alignment of trees: an alternative to tree edit
Theoretical Computer Science
The Tree-to-Tree Correction Problem
Journal of the ACM (JACM)
Computing the Edit-Distance between Unrooted Ordered Trees
ESA '98 Proceedings of the 6th Annual European Symposium on Algorithms
Computing Similarity Between RNA Secondary Structures
INTSYS '98 Proceedings of the IEEE International Joint Symposia on Intelligence and Systems
Local Similarity in RNA Secondary Structures
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
Algorithms for finding a most similar subforest
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
A linear tree edit distance algorithm for similar ordered trees
CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
Local gapped subforest alignment and its application in finding RNA structural motifs
ISAAC'04 Proceedings of the 15th international conference on Algorithms and Computation
An optimal decomposition algorithm for tree edit distance
ICALP'07 Proceedings of the 34th international conference on Automata, Languages and Programming
Algorithms for local similarity between forests
Journal of Combinatorial Optimization
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Ordered labelled trees are trees where the left-to-right order among siblings is significant. An ordered labelled forest is a sequence of ordered labelled trees. Given an ordered labelled forest F ("the target forest") and an ordered labelled forest G ("the pattern forest"), the forest pattern matching problem is to find a sub-forest F′ of F such that F′ and G are the most similar over all possible F′. In this paper, we present efficient algorithms for the forest pattern matching problem for two types of sub-forests: closed subforests and closed substructures. As RNA molecules' secondary structures could be represented as ordered labelled forests, our algorithms can be used to locate the structural or functional regions in RNA secondary structures.