It has become clear recently that there are many RNAs that are not translated into proteins, instead they work as functional molecules. These RNAs are called “non-coding RNAs.” Predicting the secondary structure of these RNAs is important for understanding their functions. We will therefore focus on Nussinov’s algorithm and the SCFG version of Nussinov’s algorithm as useful techniques for predi...

Algorithms for prediction of RNA secondary structure— the set of base pairsthat form when an RNA molecule folds— are valuable to biologists who aim tounderstand RNA structure and function. Improving the accuracy and efficiencyof prediction methods is an ongoing challenge, particularly for pseudoknottedsecondary structures, in which base pairs overlap. This challenge is biologica...

A secondary structure model for 23S ribosomal RNA has been constructed on the basis of comparative sequence data, including the complete sequences from E. coli. Bacillus stearothermophilis, human and mouse mitochondria and several partial sequences. The model has been tested extensively with single strand-specific chemical and enzymatic probes. Long range base-paired interactions organize the m...

The secondary structure of the P5abc subdomain (a 56-nt RNA) of the Tetrahymena thermophila group I intron ribozyme has been determined by NMR. Its base pairing in aqueous solution in the absence of magnesium ions is significantly different from the RNA in a crystal but is consistent with thermodynamic predictions. On addition of magnesium ions, the RNA folds into a tertiary structure with grea...

RNAbow diagrams are a versatile tool for visualizing and comparing ensembles of RNA secondary structures. Previously, RNAbows have proved useful when investigating individual ensembles of folds, performing cluster analysis, and identifying conformational changes caused by single nucleotide polymorphisms [Aalberts and Jannen, RNA, 19, 475–478 (2013)]. This contest submission highlights their use...

The range of roles played by structured RNAs in biological systems is vast. At the same time as we are learning more about the importance of RNA structure, recent advances in reagents, methods and technology mean that RNA secondary structural probing has become faster and more accurate. As a result, the capabilities of laboratories that already perform this type of structural analysis have incr...

The secondary structures of the RNAs from the signal recognition particle, termed SRP-RNA, were derived buy comparative analyses of an alignment of 39 sequences. The models are minimal in that only base pairs are included for which there is comparative evidence. The structures represent refinements of earlier versions and include a new short helix.

Several state-of-the-art tools for predicting RNA secondary structures have worst-case time and space requirements of O(n3) and O(n2) for sequence length n, limiting their applicability for practical purposes. Accordingly, biologists are interested in getting results faster, where a moderate loss of accuracy would willingly be tolerated. For this reason, we propose a novel algorithm for structu...

M.A. Roytberg, Institute of Mathematical Problems in Biology, Pushchino, Russia, Higher School of Economics, Moscow, Russia, [email protected] We propose a new definition of the loop, which on the one hand is a generalization of the definition of Mathews-Turner [1], and on the other hand allows to divide into loops an arbitrary secondary structure, not only the pseudoknot-free structure. Bas...

Predicting the secondary structure of RNA molecules from the knowledge of the primary structure (the sequence of bases) is still a challenging task. There are algorithms that provide good results e.g. based on the search for an energetic optimal configuration. However the output of such algorithms does not always give the real folding of the molecule and therefore a feature to judge the reliabi...