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Bridging the gap in RNA structure prediction
Current Opinion in Structural Biology, 2007The field of RNA structure prediction has experienced significant advances in the past several years, thanks to the availability of new experimental data and improved computational methodologies. These methods determine RNA secondary structures and pseudoknots from sequence alignments, thermodynamics-based dynamic programming algorithms, genetic ...
Bruce A, Shapiro +3 more
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Modified Nucleotides and RNA Structure Prediction
2012Nucleotide modifications are occurrent in all types of RNA and play an important role in RNA structure formation and stability. Modified bases not only possess the ability to shift the RNA structure ensemble towards desired functional confirmations. By changes in the base pairing partner preference, they may even enlarge or reduce the conformational ...
Yuliia, Varenyk, Ronny, Lorenz
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Secondary Structure Prediction for Aligned RNA Sequences
Journal of Molecular Biology, 2002Most functional RNA molecules have characteristic secondary structures that are highly conserved in evolution. Here we present a method for computing the consensus structure of a set aligned RNA sequences taking into account both thermodynamic stability and sequence covariation.
Ivo L. Hofacker +2 more
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The PTAS of Prediction for RNA Pseudoknotted Structure
2016 12th International Conference on Computational Intelligence and Security (CIS), 2016It is difficult to compute large RNA molecules with pseudoknots in bioinformatics, the prediction of RNA structure with pseudoknots is an NP-hard problem. According to PTAS principle and MFE models, we investigate the RNA pseudoknotted structure. We first presents an efficient algorithm for predicting RNA structure with pseudoknots.
Zhendong Liu +5 more
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RNA Consensus Structure Prediction With RNAalifold
2007The secondary structure of most functional RNA molecules is strongly conserved in evolution. Prediction of these conserved structures is therefore of particular interest when studying noncoding RNAs. Moreover, structure predictions on the basis of several sequences produce much more accurate results than energy directed folding of single sequences. The
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On the parallel prediction of the RNA secondary structure
2004Publisher Summary This chapter discusses the parallelization of the Vienna package algorithm that predicts the secondary structure of the RNA. Before the tool can be effectively used, it must be tuned on the target architecture. This tune consists of finding the tile sizes for optimal executions.
Francisco Almeida +5 more
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Computational Prediction of RNA Secondary Structure
2013The purpose of this section is to detail methods for the computational prediction of RNA secondary structure. This protocol is intended to provide an easy entry into the field of RNA structure prediction for those wishing to utilize it in their research and to suggest 'best practices' for going from sequence to secondary structure depending on the ...
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RNA Structure Prediction: An Overview of Methods
2012RNA is now appreciated to serve numerous cellular roles, and understanding RNA structure is important for understanding a mechanism of action. This contribution discusses the methods available for predicting RNA structure. Secondary structure is the set of the canonical base pairs, and secondary structure can be accurately determined by comparative ...
Matthew G, Seetin, David H, Mathews
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Revolutions in RNA Secondary Structure Prediction
Journal of Molecular Biology, 2006RNA structure formation is hierarchical and, therefore, secondary structure, the sum of canonical base-pairs, can generally be predicted without knowledge of the three-dimensional structure. Secondary structure prediction algorithms evolved from predicting a single, lowest free energy structure to their current state where statistics can be determined ...
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Prediction of Sequentially Optimal RNA Secondary Structures
Journal of Biomolecular Structure and Dynamics, 1997A rigorous mathematical modeling of the RNA sequential folding process during transcription is proposed. It is based, at each transcription step, on a homogeneous markovian jump process, the state space of which is the set of structures constructible on the part of the RNA already transcribed.
Breton, N., Jacob, C., Daegelen, P.
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