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
A global parser for context-free phrase structure grammars
Communications of the ACM
Information Processing Letters
Local Similarity in RNA Secondary Structures
CSB '03 Proceedings of the IEEE Computer Society Conference on Bioinformatics
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)
An algebraic view of the relation between largest common subtrees and smallest common supertrees
Theoretical Computer Science
Fixed Parameter Tractable Alignment of RNA Structures Including Arbitrary Pseudoknots
CPM '08 Proceedings of the 19th annual symposium on Combinatorial Pattern Matching
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Fast RNA Structure Alignment for Crossing Input Structures
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
Multiple genome alignment: chaining algorithms revisited
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Semantics and Ambiguity of Stochastic RNA Family Models
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Bellman's GAP: a declarative language for dynamic programming
Proceedings of the 13th international ACM SIGPLAN symposium on Principles and practices of declarative programming
How to compare arc-annotated sequences: the alignment hierarchy
SPIRE'06 Proceedings of the 13th international conference on String Processing and Information Retrieval
A linear tree edit distance algorithm for similar ordered trees
CPM'05 Proceedings of the 16th annual conference on Combinatorial Pattern Matching
| Hi-index | 5.23 |
We present two enhancements to Jiang's tree alignment algorithm, motivated by experience with its use for RNA structure alignment. One enhancement is the introduction of an affine gap model, which can be accommodated with a runtime increase by a constant factor. The second enhancement is a speed-up of the alignment algorithm when certain nodes in the trees are pre-aligned by a so-called anchoring. Both enhancements are included in a new implementation of the tool RNAforester. We evaluate the new algorithm with two applications related to RNA secondary structure analysis. Based on our experience, we suggest a new formulation of the tree alignment model, based on regular tree languages and rewrite rules.