Efficient chaining of seeds in ordered trees

Authors:
Julien Allali;Cédric Chauve;Pascal Ferraro;Anne-Laure Gaillard
Affiliations:
LaBRI, Université Bordeaux 1, IPB, CNRS and Pacific Institute for Mathematical Sciences and CNRS UMI3069 and Department of Mathematics, Simon Fraser University;Department of Mathematics, Simon Fraser University;LaBRI, Université Bordeaux 1, IPB, CNRS, and Pacific Institute for Mathematical Sciences and CNRS UMI3069 and Department of Computer Science, University of Calgary;LaBRI, Université Bordeaux 1, IPB, CNRS
Venue:
IWOCA'10 Proceedings of the 21st international conference on Combinatorial algorithms
Year:
2010

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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.