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
On the complexity of comparing evolutionary trees
Discrete Applied Mathematics - Special volume on computational molecular biology
The Tree-to-Tree Correction Problem
Journal of the ACM (JACM)
Computing Similarity Between RNA Secondary Structures
INTSYS '98 Proceedings of the IEEE International Joint Symposia on Intelligence and Systems
Computing the similarity of two sequences with nested arc annotations
Theoretical Computer Science
An Algorithm for Detecting Homologues of Known Structured RNAs in Genomes
CSB '04 Proceedings of the 2004 IEEE Computational Systems Bioinformatics Conference
A remark on the subsequence problem for arc-annotated sequences with pairwise nested arcs
Information Processing Letters
Kernel design for RNA classification using Support Vector Machines
International Journal of Data Mining and Bioinformatics
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A new algorithm for aligning nested arc-annotated sequences under arbitrary weight schemes
Theoretical Computer Science
Parameterized complexity of the arc-preserving subsequence problem
WG'10 Proceedings of the 36th international conference on Graph-theoretic concepts in computer science
RTED: a robust algorithm for the tree edit distance
Proceedings of the VLDB Endowment
How to compare arc-annotated sequences: the alignment hierarchy
SPIRE'06 Proceedings of the 13th international conference on String Processing and Information Retrieval
Faster pattern matching algorithm for arc-annotated sequences
Proceedings of the 2005 international conference on Federation over the Web
Algorithms for local forest similarity
ISAAC'05 Proceedings of the 16th international conference on Algorithms and Computation
RNA-RNA interaction prediction and antisense RNA target search
RECOMB'05 Proceedings of the 9th Annual international conference on Research in Computational Molecular Biology
RNA secondary structure prediction via energy density minimization
RECOMB'06 Proceedings of the 10th annual international conference on Research in Computational Molecular Biology
| Hi-index | 5.23 |
The primary structure of a ribonucleic acid (RNA) molecule is a sequence of nucleotides (bases) over the four-letter 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 AU and CG. 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, for tertiary structures, it is Max SNP-hard for both minimization and maximization versions. We show a stronger result for the maximization version where it cannot be approximated within ratio 2logn in polynomial time, unless NPDTIME[2polylogn]. We then present an algorithm that can be used for practical application. Our algorithm will produce an optimal solution for the case where at least one of the RNA involved is of a secondary structure. We also show an approximation algorithm.