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Published in:
2012 | OriginalPaper | Chapter
Tree Decomposition and Parameterized Algorithms for RNA Structure-Sequence Alignment Including Tertiary Interactions and Pseudoknots
(Extended Abstract)
Authors : Philippe Rinaudo, Yann Ponty, Dominique Barth, Alain Denise
Published in: Algorithms in Bioinformatics
Publisher: Springer Berlin Heidelberg
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We present a general setting for structure-sequence comparison in a large class of RNA structures, that unifies and generalizes a number of recent works on specific families of structures. Our approach is based on a
tree decomposition
of structures, and gives rise to a general parameterized algorithm having complexity in
$\mathcal{O}(N\cdot m^t)$
, where
N
(resp.
m
) is the structure (resp. sequence) length, and the exponent
t
depends on the family of structures. For each family considered by previous approaches, our contribution specializes into an algorithm whose complexity either matches or outperforms previous solutions.