Efficient chaining of seeds in ordered trees

Details Efficient chaining of seeds in ordered trees Efficient chaining of seeds in ordered trees

2010-07-06

arxiv.org/abs/1007.0942v1

21st International Workshop on Combinatorial Algorithms, London : United Kingdom (2010)

Biology

Quantitative Biology

Quantitative Methods

Scientific paper

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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