Structural alignment of large—size proteins via lagrangian relaxation
Proceedings of the sixth annual international conference on Computational biology
On global warming: Flow-based soft global constraints
Journal of Heuristics
AND/OR Branch-and-Bound search for combinatorial optimization in graphical models
Artificial Intelligence
Extending the hardness of RNA secondary structure comparison
ESCAPE'07 Proceedings of the First international conference on Combinatorics, Algorithms, Probabilistic and Experimental Methodologies
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The optimization of weighted string alignments is a well studied problem recurring in a number of application domains and can be solved efficiently. The problem becomes MAX-SNP-hard as soon as arbitrary pairwise dependencies among the alignment edges are introduced. We present a global propagator for this problem which is based on efficiently solving a relaxation of it. In the context of bioinformatics, the problem is known as alignment of arc-annotated sequences, which is e.g. used for comparing RNA molecules. For a restricted version of this alignment problem, we show that a constraint program based on our propagator is on par with state of the art methods. For the general problem with unrestricted dependencies, our tool constitutes the first available method with promising applications in this field.