2017
DOI: 10.1093/bioinformatics/btx783
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New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation

Abstract: MotivationUnderstanding the formation, architecture and roles of pseudoknots in RNA structures are one of the most difficult challenges in RNA computational biology and structural bioinformatics. Methods predicting pseudoknots typically perform this with poor accuracy, often despite experimental data incorporation. Existing bioinformatic approaches differ in terms of pseudoknots’ recognition and revealing their nature. A few ways of pseudoknot classification exist, most common ones refer to a genus or order. F… Show more

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Cited by 40 publications
(48 citation statements)
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“…It will help in broadening the range of possible 3D structure modifications and introduce more flexibility into the remodeling process. Such a change can improve the accuracy of predicting the pseudoknotted RNA structures which currently constitute quite a significant problem of computational prediction methods [ 51 ]. Future plans include also implementation of procedures to support modified residues in the input RNA structure.…”
Section: Discussionmentioning
confidence: 99%
“…It will help in broadening the range of possible 3D structure modifications and introduce more flexibility into the remodeling process. Such a change can improve the accuracy of predicting the pseudoknotted RNA structures which currently constitute quite a significant problem of computational prediction methods [ 51 ]. Future plans include also implementation of procedures to support modified residues in the input RNA structure.…”
Section: Discussionmentioning
confidence: 99%
“…The user can also decide how to treat non-canonical and isolated base pairs which strongly impact pseudoknot orders and structure topology. The second step has been recently introduced and has five algorithms, Hybrid Algorithm (default), Dynamic Programming, Elimination Min-Gain, Elimination Max-Conflicts, First-Come-First-Served ( 16 ), to support high-order pseudoknot processing. They follow different routines to find the optimum nested substructure, identify pseudoknot orders and encode the secondary structure topology in extended dot-bracket notation.…”
Section: Methods Outlinementioning
confidence: 99%
“…This paper presents RNApolis, a new computing platform that collects bioinformatics tools developed by the RNA bioinformatics group of researchers affiliated at the Institute of Computing Science, Poznan University of Technology and the Institute of Bioorganic Chemistry, Polish Academy of Sciences. The following RNA-dedicated tools are accessible via the platform: RNA FRABASE [42,43], RNAComposer [4,44,46], RNApdbee [5,59], RNAlyzer [30], RNAssess [31], RNAfitme [5,6,58], and RNAvista [7]. They aim to support the research which focuses on the secondary and the tertiary structure of RNA molecules.…”
Section: Figure 1 Sequence Secondary and Tertiary Structure Data Ofmentioning
confidence: 99%
“…RNA structure is hierarchical ( Figure 1) [5,14]. This hierarchy allows the architecture and properties of a molecule to be studied from partial knowledge, which is often sufficient to draw basic conclusions [13,35].…”
Section: Introductionmentioning
confidence: 99%
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