Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots

Authors:
Philippe Rinaudo;Yann Ponty;Dominique Barth;Alain Denise
Affiliations:
LRI, Univ Paris-Sud, CNRS UMR8623 and INRIA AMIB, Orsay, France,PRISM, Univ Versailles Saint-Quentin and CNRS UMR8144 Versailles, France;LIX, Ecole Polytechnique, CNRS UMR7161 and INRIA AMIB, Palaiseau, France;PRISM, Univ Versailles Saint-Quentin and CNRS UMR8144 Versailles, France;LRI, Univ Paris-Sud, CNRS UMR8623 and INRIA AMIB, Orsay, France,IGM, Univ Paris-Sud and CNRS UMR8621, Orsay, France
Venue:
WABI'12 Proceedings of the 12th international conference on Algorithms in Bioinformatics
Year:
2012

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Abstract

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.