Generalization of a Suffix Tree for RNA Structural Pattern Matching |
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Authors: | Email author" target="_blank">Tetsuo?ShibuyaEmail author |
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Affiliation: | (1) IBM Tokyo Research Laboratory, 1623-14 Shimotsuruma, Yamato-shi, Kanagawa 242-8502, Japan |
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Abstract: | In molecular biology, it is said that
two biological sequences tend to have similar properties if they have similar
three-dimensional 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.
We call it the structural suffix tree or s-suffix tree for short.
The s-suffix tree can be used for finding structurally related patterns of RNA
or single-stranded DNA.
Furthermore, we propose an
O(n(log| | + log| |)) on-line algorithm for constructing it,
where n is the sequence length,
| | is the size of the normal alphabet, and | | is that of the
alphabet called parameter, which is related to the structure of the sequence.
Our algorithm achieves 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 the 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. |
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Keywords: | Pattern matching Suffix tree generalization Parameterized suffix
tree Computational biology RNA structure matching |
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