Fast algorithms for finding nearest common ancestors
SIAM Journal on Computing
Parameterized pattern matching: algorithms and applications
Journal of Computer and System Sciences
Algorithms on strings, trees, and sequences: computer science and computational biology
Algorithms on strings, trees, and sequences: computer science and computational biology
Parameterized Duplication in Strings: Algorithms and an Application to Software Maintenance
SIAM Journal on Computing
A polyhedral approach to RNA sequence structure alignment
RECOMB '98 Proceedings of the second annual international conference on Computational molecular biology
Internal loops in RNA secondary structure prediction
RECOMB '99 Proceedings of the third annual international conference on Computational molecular biology
Parameterized pattern matching by Boyer-Moore-type algorithms
Proceedings of the sixth annual ACM-SIAM symposium on Discrete algorithms
Proceedings of the tenth annual ACM-SIAM symposium on Discrete algorithms
Proceedings of the tenth annual ACM-SIAM symposium on Discrete algorithms
A Space-Economical Suffix Tree Construction Algorithm
Journal of the ACM (JACM)
The Design and Analysis of Computer Algorithms
The Design and Analysis of Computer Algorithms
A Phylogenetic Approach to RNA Structure Prediction
Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology
Faster algorithms for the construction of parameterized suffix trees
FOCS '95 Proceedings of the 36th Annual Symposium on Foundations of Computer Science
Optimal suffix tree construction with large alphabets
FOCS '97 Proceedings of the 38th Annual Symposium on Foundations of Computer Science
Linear pattern matching algorithms
SWAT '73 Proceedings of the 14th Annual Symposium on Switching and Automata Theory (swat 1973)
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In molecular biology, it is said that two biological sequences tend to have similar properties if they have similar 3-D structures. Hence, it is very important to find not only similar sequences in the string sense, but also structurally similar sequences from databases. In this paper, we propose a new data structure that is a generalization of a parameterized suffix tree (p-suffix tree for short) introduced by Baker. This data structure can be used for finding structurally related patterns of RNA or single-stranded DNA. Furthermore, we propose an O(n(log |Σ|+log |Π|)) on-line algorithm for constructing it, where n is the sequence length, |Σ| is the size of the normal alphabet, and |Π| is that of the alphabet called "parameter," which is related to the structure of the sequence. Our algorithm achieves a linear time when it is used to analyze RNA and DNA sequences. Furthermore, as an algorithm for constructing the p-suffix tree, it is the first on-line algorithm, though the computing bound of our algorithm is same as that of Kosaraju's best-known algorithm. The results of computational experiments using actual RNA and DNA sequences are also given to demonstrate our algorithm's practicality.