Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Approximate matching of secondary structures
Proceedings of the sixth annual international conference on Computational biology
Computing similarity between RNA structures
Theoretical Computer Science
Flexible pattern matching in strings: practical on-line search algorithms for texts and biological sequences
SPIRE 2002 Proceedings of the 9th International Symposium on String Processing and Information Retrieval
Pattern Matching for Arc-Annotated Sequences
FST TCS '02 Proceedings of the 22nd Conference Kanpur on Foundations of Software Technology and Theoretical Computer Science
Finding Common Subsequences with Arcs and Pseudoknots
CPM '99 Proceedings of the 10th Annual Symposium on Combinatorial Pattern Matching
On the computational complexity of 2-interval pattern matching problems
Theoretical Computer Science
Computing the similarity of two sequences with nested arc annotations
Theoretical Computer Science
Building a bioinformatics ontology using OIL
IEEE Transactions on Information Technology in Biomedicine
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
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We present an improvement of pattern matching algorithm for arc-annotated sequences. Arc-annotated sequences are used for representing the structural information, e.g., RNA and protein sequences in molecular biology. Given two sequences with arcs, a text of length n and a pattern of length m, the problem is to determine whether the pattern is an arc-preserving subsequence of the text. Although it is NP-complete in a general case, an O(mn) algorithm has been proposed if the given sequences have no crossing-arcs. Our contribution is to revise it and to obtain more simple one. We also present our experimental results of the running time.