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We present a general setting for structure-sequence comparison in a largeclass of RNA structures that unifies and generalizes a number of recent workson specific families on structures. Our approach is based on tree decompositionof structures and gives rises to a general parameterized algorithm, where theexponential part of the complexity depends on the family of structures. Foreach of the previously studied families, our algorithm has the same complexityas the specific algorithm that had been given before.

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