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arXiv · 1007.0942

Efficient chaining of seeds in ordered trees

Julien Allali·Cédric Chauve·Pascal Ferraro·Anne-Laure Gaillard
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Abstract

We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem is a natural extension of a similar problem for sequences, and has applications in computational biology, such as mining a database of RNA secondary structures. For the chaining problem with a set of m constant size seeds, we describe an algorithm with complexity O(m2 log(m)) in time and O(m2) in space.

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Julien Allali, Cédric Chauve, Pascal Ferraro, Anne-Laure Gaillard. 2010-07-06. Efficient chaining of seeds in ordered trees. https://doi.org/10.1007/978-3-642-19222-7_27

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