Efficient chaining of seeds in ordered trees

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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Submitted on : Thursday, June 24, 2010 - 11:10:18 PM
Last modification on : Wednesday, June 26, 2019 - 4:28:03 PM
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  • HAL Id : hal-00490028, version 1
  • ARXIV : 1007.0942

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Julien Allali, Cédric Chauve, Pascal Ferraro, Anne-Laure Gaillard. Efficient chaining of seeds in ordered trees. 21st International Workshop on Combinatorial Algorithms, Jul 2010, London, United Kingdom. ⟨hal-00490028⟩

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