TAILIEUCHUNG - Báo cáo sinh học: "Sparsification of RNA structure prediction including pseudoknots"

Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí y học Molecular Biology cung cấp cho các bạn kiến thức về ngành sinh học đề tài: Sparsification of RNA structure prediction including pseudoknots. | Mõhl et al. Algorithms for Molecular Biology 2010 5 39 http content 5 1 39 AMR ALGORITHMS FOR MOLECULAR BIOLOGY RESEARCH Open Access Sparsification of RNA structure prediction including pseudoknots l -d1tP bQlQl i 21 1 4 v 2 Mathias MOhl raneien saiari Sebastian will Rolf oacKOTen S CenK baninaip Abstract 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. Background Recently discovered catalytic and regulatory RNAs 1 2 exhibit their functionality due to specific secondary and tertiary structures 3 4 . The vast majority of computational analysis of non-coding RNAs have been restricted to nested secondary structures neglecting pseudoknots -which are among the most prevalent RNA structures 5 . For example Xaya-phoummine et al. 6 estimated that up to 30 of the base pairs .

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