Efficient chaining of seeds in ordered trees

Authors:
Julien Allali;Cedric Chauve;Pascal Ferraro;Anne-Laure Gaillard
Affiliations:
LaBRI, Université Bordeaux 1, CNRS UMR 5800, Talence, France and Pacific Institute for Mathematical Sciences, CNRS UMI 3069, Vancouver, BC, Canada and Department of Mathematics, Simon Fraser ...;Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada;LaBRI, Université Bordeaux 1, CNRS UMR 5800, Talence, France and Pacific Institute for Mathematical Sciences, CNRS UMI 3069, Vancouver, BC, Canada and Department of Computer Science, Universi ...;LaBRI, Université Bordeaux 1, CNRS UMR 5800, Talence, France
Venue:
Journal of Discrete Algorithms
Year:
2012

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Abstract

We consider 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 S of m seeds of cumulated size @?S@?, we describe an algorithm with complexity O(@?S@?log(@?S@?)+m@?S@?log(m)) in time and O(m@?S@?) in space.