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Alignnment of RNA with Structures of Unlimited Complexity

Sequence-structure alignment of RNAs with arbitrary secondary structures is Max-SNP-hard. Therefore, the problem of RNA alignment is commonly restricted to nested structure, where dynamic programming yields efficient solutions. However, nested structure cannot model pseudoknots or even more complex structural dependencies. Nevertheless those dependencies are essential and conserved features of many RNAs. Only few existing approaches deal with crossings of limited complexity or arbitrary crossing structures. Here, we present a constraint approach for alignment of structures in the even more general class of structures with unlimited complexity. Our central contribution is a new RNA alignment propagator. It is based on an efficient O(n<sup>2</sup>) relaxation of the RNA alignment problem. Specifically, our approach Carna solves the alignment problem for sequences with given input structure of unlimited complexity. Carna is implemented using Gecode.