Ordered and Unordered Tree Inclusion
SIAM Journal on Computing
Approximate matching of secondary structures
Proceedings of the sixth annual international conference on Computational biology
The Longest Common Subsequence Problem for Sequences with Nested Arc Annotations
ICALP '01 Proceedings of the 28th International Colloquium on Automata, Languages and Programming,
Pattern Matching Problems over 2-Interval Sets
CPM '02 Proceedings of the 13th Annual Symposium on Combinatorial Pattern Matching
CPM '02 Proceedings of the 13th Annual Symposium on Combinatorial Pattern Matching
Finding Common Subsequences with Arcs and Pseudoknots
CPM '99 Proceedings of the 10th Annual Symposium on Combinatorial Pattern Matching
The Longest Common Subsequence Problem for Arc-Annotated Sequences
COM '00 Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching
Computing the similarity of two sequences with nested arc annotations
Theoretical Computer Science
A Polynomial-Time Algorithm for the Matching of Crossing Contact-Map Patterns
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
A remark on the subsequence problem for arc-annotated sequences with pairwise nested arcs
Information Processing Letters
Fast detection of common sequence structure patterns in RNAs
Journal of Discrete Algorithms
Extracting constrained 2-interval subsets in 2-interval sets
Theoretical Computer Science
Approximating the 2-interval pattern problem
Theoretical Computer Science
Fast Arc-Annotated Subsequence Matching in Linear Space
SOFSEM '10 Proceedings of the 36th Conference on Current Trends in Theory and Practice of Computer Science
Comparing RNA structures: towards an intermediate model between the edit and the LAPCS problems
BSB'07 Proceedings of the 2nd Brazilian conference on Advances in bioinformatics and computational biology
Finding common structured patterns in linear graphs
Theoretical Computer Science
Approximation of RNA multiple structural alignment
Journal of Discrete Algorithms
Approximation of RNA multiple structural alignment
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
Faster pattern matching algorithm for arc-annotated sequences
Proceedings of the 2005 international conference on Federation over the Web
Finding exact and maximum occurrences of protein complexes in protein-protein interaction graphs
MFCS'05 Proceedings of the 30th international conference on Mathematical Foundations of Computer Science
Local gapped subforest alignment and its application in finding RNA structural motifs
ISAAC'04 Proceedings of the 15th 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
Normalized similarity of RNA sequences
SPIRE'05 Proceedings of the 12th international conference on String Processing and Information Retrieval
Common structured patterns in linear graphs: approximation and combinatorics
CPM'07 Proceedings of the 18th annual conference on Combinatorial Pattern Matching
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A study of pattern matching for arc-annotated sequences is started. An O(nm) time algorithm is given to determine whether a length m sequence with nested arc annotations is an arc-preserving subsequence of a length n sequence with nested arc annotations, called APS(NESTED,NESTED). Arc-annotated sequences and, in particular, those with nested arc structure are motivated by applications in RNA structure comparison. Our algorithm can be used to accelerate a recent fixed-parameter algorithm for LAPCS(NESTED,NESTED) and generalizes results for ordered tree inclusion problems. In particular, the presented dynamic programming methodology implies a quadratic time algorithm for an open problem posed by Vialette.