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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: Inverse folding of RNA pseudoknot structures. | Gao et al. Algorithms for Molecular Biology 2010 5 27 http www.almob.Org content 5 1 27 AMR ALGORITHMS FOR MOLECULAR BIOLOGY RESEARCH Open Access Inverse folding of RNA pseudoknot structures James ZM Gao Linda YM Li Christian M Reidys Abstract Background RNA exhibits a variety of structural configurations. Here we consider a structure to be tantamount to the noncrossing Watson-Crick and G-U-base pairings secondary structure and additional cross-serial base pairs. These interactions are called pseudoknots and are observed across the whole spectrum of RNA functionalities. In the context of studying natural RNA structures searching for new ribozymes and designing artificial RNA it is of interest to find RNA sequences folding into a specific structure and to analyze their induced neutral networks. Since the established inverse folding algorithms RNAinverse RNA-SSD as well as INFO-RNA are limited to RNA secondary structures we present in this paper the inverse folding algorithm Inv which can deal with 3-noncrossing canonical pseudoknot structures. Results In this paper we present the inverse folding algorithm Inv. We give a detailed analysis of Inv including pseudocodes. We show that Inv allows to design in particular 3-noncrossing nonplanar RNA pseudoknot 3-noncrossing RNA structures-a class which is difficult to construct via dynamic programming routines. Inv is freely available at http www.combinatorics.cn cbpc inv.html. Conclusions The algorithm Inv extends inverse folding capabilities to RNA pseudoknot structures. In comparison with RNAinverse it uses new ideas for instance by considering sets of competing structures. As a result Inv is not only able to find novel sequences even for RNA secondary structures it does so in the context of competing structures that potentially exhibit cross-serial interactions. 1 Introduction Pseudoknots are structural elements of central importance in RNA structures 1 see Figure 1. They represent cross-serial base pairing interactions
