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 editing distance between unordered labeled trees
Information Processing Letters
Alignment of trees: an alternative to tree edit
Theoretical Computer Science
Pattern matching algorithms
An Algorithm for Finding the Largest Approximately Common Substructures of Two Trees
IEEE Transactions on Pattern Analysis and Machine Intelligence
The String-to-String Correction Problem
Journal of the ACM (JACM)
The Tree-to-Tree Correction Problem
Journal of the ACM (JACM)
Identifying approximately common substructures in trees based on a restricted edit distance
Information Sciences: an International Journal
Identifying consensus of trees through alignment
Information Sciences—Informatics and Computer Science: An International Journal
AMAST '02 Proceedings of the 9th International Conference on Algebraic Methodology and Software Technology
A Fast Algorithm for Optimal Alignment between Similar Ordered Trees
CPM '01 Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching
A New Editing based Distance between Unordered Labeled Trees
CPM '93 Proceedings of the 4th Annual Symposium on Combinatorial Pattern Matching
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
Mining protein family specific residue packing patterns from protein structure graphs
RECOMB '04 Proceedings of the eighth annual international conference on Resaerch in computational molecular biology
A discipline of dynamic programming over sequence data
Science of Computer Programming - Methods of software design: Techniques and applications
Pure Multiple RNA Secondary Structure Alignments: A Progressive Profile Approach
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Prediction of Consensus RNA Secondary Structures Including Pseudoknots
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A New Distance for High Level RNA Secondary Structure Comparison
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Searching Genomes for Noncoding RNA Using FastR
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
Local similarity between quotiented ordered trees
Journal of Discrete Algorithms
Fast detection of common sequence structure patterns in RNAs
Journal of Discrete Algorithms
Comparing similar ordered trees in linear-time
Journal of Discrete Algorithms
Computational Biology and Chemistry
A multiple layer model to compare RNA secondary structures
Software—Practice & Experience
A local tree alignment-based soft pattern matching approach for information extraction
NAACL-Short '09 Proceedings of Human Language Technologies: The 2009 Annual Conference of the North American Chapter of the Association for Computational Linguistics, Companion Volume: Short Papers
Web corpus mining by instance of Wikipedia
WAC '06 Proceedings of the 2nd International Workshop on Web as Corpus
Stability of RNA structural motifs and its influence on editing efficiency by adenosine deaminases
International Journal of Bioinformatics Research and Applications
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Algorithms for forest pattern matching
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
A new algorithm for aligning nested arc-annotated sequences under arbitrary weight schemes
Theoretical Computer Science
A local tree alignment approach to relation extraction of multiple arguments
Information Processing and Management: an International Journal
Forest alignment with affine gaps and anchors
CPM'11 Proceedings of the 22nd 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
Algorithms for finding a most similar subforest
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
Algorithms for local forest similarity
ISAAC'05 Proceedings of the 16th international conference on Algorithms and Computation
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 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
Exact pattern matching for RNA structure ensembles
RECOMB'12 Proceedings of the 16th Annual international conference on Research in Computational Molecular Biology
RNA tree comparisons via unrooted unordered alignments
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
Coloring based approach for matching unrooted and/or unordered trees
Pattern Recognition Letters
Forest alignment with affine gaps and anchors, applied in RNA structure comparison
Theoretical Computer Science
Algorithms for local similarity between forests
Journal of Combinatorial Optimization
| Hi-index | 0.00 |
We present a systematic treatment of alignment distanceand local similarity algorithms on trees and forests. Webuild upon the tree alignment algorithm for ordered treesgiven by Jiang et. al (1995) and extend it to calculate localforest alignments, which is essential for finding localsimilar regions in RNA secondary structures. The timecomplexity of our algorithm is O(|F1| \cdot |F2 \cdot deg(F1) \cdotdeg(F2) \cdot (deg(F1) + deg(F2)) where |Fi| is the number of nodes in forest Fi and deg (Fi) is the degree of Fi. Weprovide carefully engineered dynamic programming implementationsusing dense, two-dimensional tables which considerablyreduces the space requirement. We suggest anew representation of RNA secondary structures as foreststhat allow reasonable scoring of edit operations on RNAsecondary structures. The comparison of RNA secondarystructures is facilitated by a new visualization technique forRNA secondary structure alignments. Finally, we show howpotential regulatory motifs can be discovered solely by theirstructural preservation, and independent of their sequenceconservation and position.