Abstract
RNA interactions are fundamental in many cellular processes, which can involve two or more RNA molecules. Multiple RNA interactions are also believed to be much more complex than pairwise interactions. Recently, multiple RNA interaction prediction has been formulated as a maximization problem. Here we extensively examine this optimization problem under several biologically meaningful interaction models. We present a polynomial time algorithm for the problem when the order of interacting RNAs is known and pseudoknot interactions are allowed; for the general problem without an assumed RNA order, we prove the NP-hardness for both variants (allowing and disallowing pseudoknot interactions), and present a constant ratio approximation algorithm for each of them.
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