Efficient chaining of seeds in ordered trees

Julien Allali (1) , Cédric Chauve (2) , Pascal Ferraro (1, 3) , Anne-Laure Gaillard (1)

1 LaBRI - Laboratoire Bordelais de Recherche en Informatique
2 SFU - Department of Mathematics [Burnaby]
3 PIMS - Pacific Institute for the Mathematical Sciences

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.

Domaines: Bio-Informatique, Biologie Systémique [q-bio.QM]; Bio-informatique [q-bio.QM]

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⟩