Tree graphs of RNA secondary structures and their comparisons
Computers and Biomedical Research
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)
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
The Longest Common Subsequence Problem for Arc-Annotated Sequences
COM '00 Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching
Multiple RNA Structure Alignment
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
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
Space efficient algorithms for ordered tree comparison
ISAAC'05 Proceedings of the 16th international conference on Algorithms and Computation
What makes the arc-preserving subsequence problem hard?
ICCS'05 Proceedings of the 5th international conference on Computational Science - Volume Part II
What makes the arc-preserving subsequence problem hard?
Transactions on Computational Systems Biology II
Local exact pattern matching for non-fixed RNA structures
CPM'12 Proceedings of the 23rd Annual conference on Combinatorial Pattern Matching
Seeded tree alignment and planar tanglegram layout
WABI'07 Proceedings of the 7th international conference on Algorithms in Bioinformatics
RNA tree comparisons via unrooted unordered alignments
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
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The primary structure of a ribonucleic acid (RNA) molecule is a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base-pairs (nucleotide pairs) which forms bonds between A - U and C - G. For secondary structures, these bonds have been traditionally assumed to be one-to-one and non-crossing. This paper considers a notion of similarity between two RNA molecule structures taking into account the primary, the secondary and the tertiary structures. We show that in general this problem is NP-hard for tertiary structures. We present algorithms for the case where at least one of the RNA involved is of secondary structures. We then show that this algorithm might be used to deal with the practical application. We also show an approximation algorithm.