Sparsification of RNA structure prediction including pseudoknots

BACKGROUND: Although many RNA molecules contain pseudoknots, computational prediction of pseudoknotted RNA structure is still in its infancy due to high running time and space consumption implied by the dynamic programming formulations of the problem. RESULTS: In this paper, we introduce sparsification to significantly speedup the dynamic programming approaches for pseudoknotted RNA structure prediction, which also lower the space requirements. Although sparsification has been applied to a number of RNA-related structure prediction problems in the past few years, we provide the first application of sparsification to pseudoknotted RNA structure prediction specifically and to handling gapped fragments more generally - which has a much more complex recursive structure than other problems to which sparsification has been applied. We analyse how to sparsify four pseudoknot structure prediction algorithms, among those the most general method available (the Rivas-Eddy algorithm) and the fastest one (Reeder-Giegerich algorithm). In all algorithms the number of "candidate" substructures to be considered is reduced. CONCLUSIONS: Our experimental results on the sparsified Reeder-Giegerich algorithm suggest a linear speedup over the unsparsified implementation.