Tree decomposition and parameterized algorithms for RNA   structure-sequence alignment including tertiary interactions and pseudoknots
  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 on structures. Our approach is based on tree decomposition of structures and gives rises to a general parameterized algorithm, where the exponential part of the complexity depends on the family of structures. For each of the previously studied families, our algorithm has the same complexity as the specific algorithm that had been given before. 
Philippe Rinaudo (LRI, INRIA Saclay - Ile de France, PRISM), Yann   Ponty (INRIA Saclay - Ile de France, LIX), Dominique Bar...
q-bio.QM cs.DS