Tree decomposition and parameterized algorithms for RNA structure-sequence alignment including tertiary interactions and pseudoknots (extended abstract)

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 O(N·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. © 2012 Springer-Verlag.