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Statistics of RNA secondary structures
Biopolymers, 1993AbstractA statistical reference for RNA secondary structures with minimum free energies is computed by folding large ensembles of random RNA sequences. Four nucleotide alphabets are used: two binary alphabets, AU and GC, the biophysical AUGC and the synthetic GCXK alphabet. RNA secondary structures are made of structural elements, such as stacks, loops,
W, Fontana +3 more
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Similarity of RNA secondary structures
Journal of Computational Chemistry, 2006AbstractIn this article, we propose a relatively similar measure to compare RNA secondary structures. We first transform an RNA secondary structure into a special sequence representation. Then, on the basis of symbolic sequence complexity, we obtain the relative distance of RNA secondary structures.
Chun Li, Ai-hua Wang, Lili Xing
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Mathematical Biosciences, 1991
A mathematical model for analyzing the secondary structures of RNA is developed that is based on the connection matrix associated with the planar p-h graph. The classification of the elementary structures allows the introduction of the basis of structural space from which to build the global secondary structure.
Söler, F., Jankowski, K.
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A mathematical model for analyzing the secondary structures of RNA is developed that is based on the connection matrix associated with the planar p-h graph. The classification of the elementary structures allows the introduction of the basis of structural space from which to build the global secondary structure.
Söler, F., Jankowski, K.
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K-Partite RNA Secondary Structures
Journal of Computational Biology, 2009RNA secondary structure prediction is a fundamental problem in structural bioinformatics. The prediction problem is difficult because RNA secondary structures may contain pseudoknots formed by crossing base pairs. We introduce k-partite secondary structures as a simple classification of RNA secondary structures with pseudoknots.
Minghui Jiang 0001 +4 more
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RNA Secondary Structure an Overview
2018It was believed that the single role of the Ribonucleic acid (RNA) is to carry the information necessitate to build a specific protein. Now it discovered that RNA has important and essential roles in many gene regulatory networks and many other cellular functions.
Abdelhakim El Fatmi +4 more
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RNA Secondary Structure Thermodynamics
2012Several different ways to predict RNA secondary structures have been suggested in the literature. Statistical methods, such as those that utilize stochastic context-free grammars (SCFGs), or approaches based on machine learning aim to predict the best representative structure for the underlying ensemble of possible conformations.
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In Silico Prediction of RNA Secondary Structure
2017The secondary structure of an RNA molecule represents the base-pairing interactions within the molecule and fundamentally determines its overall structure. In this chapter, we overview the main approaches and existing tools for predicting RNA secondary structures, as well as methods for identifying noncoding RNAs from genomic sequences or RNA ...
Tahi, Fariza +2 more
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Combinatorics of Saturated Secondary Structures of RNA
Journal of Computational Biology, 2006Following Zuker (1986), a saturated secondary structure for a given RNA sequence is a secondary structure such that no base pair can be added without violating the definition of secondary structure, e.g., without introducing a pseudoknot. In the Nussinov-Jacobson energy model (Nussinov and Jacobson, 1980), where the energy of a secondary structure is ...
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Secondary structure in transfer RNA genes
Journal of Molecular Biology, 1973The bacterial strand of the heteroduplex of λh80 dglyTsu+36tyrTthrT with λh80 carries a cluster of three transfer RNA genes. The bacterial strands of the heteroduplexes of φ80hpsu+,−III and φ80hpsu−III with φ80h carry two and one genes for tyrosine tRNA, respectively.
M, Wu, N, Davidson
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Analysis of RNA Secondary Structure
2014RNA has different levels of structural organization. The primary structure is the linear order of the nucleotide monomers, the RNA sequence. During transcription process, the partially synthesized RNA is folded by base-pairing and thermodynamic intramolecular or intermolecular interactions.
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