Possible RNA secondary structures
Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures
... Albeit a crude measure, the distribution of spatial distances in thermodynamic equilibrium harbors useful information on the shape of the molecule that in turn can give insights into the interplay of its functional ...
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Random generation of RNA secondary structures according to native distributions
... random RNA secondary structures that are - related to the free energy of such structures (in expectation and variation) - in expectation ...that structures generated by our non-uniform ...
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An Adaptive Defect Weighted Sampling Algorithm to Design Pseudoknotted RNA Secondary Structures
... single RNA sequence when folded into a target pseudoknotted secondary ...it possible to characterize the equilibrium base pair qualities by computing the matrix of base pair ...pseudoknotted ...
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A Graph-Theoretical Approach for Partitioning RNA Secondary Structures into Pseudonotted and Pseudoknot-free Regions
... Pseudoknots can be classified into two main groups: standard and recursive pseudoknots [5], [19]. The latter is distinguished from the former by having nested pseudoknots within a pseudoknot. While our partitioning ...
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Selection Intensity Against Deleterious Mutations in RNA Secondary Structures and Rate of Compensatory Nucleotide Substitutions
... Parameter estimation: An important parameter of the compensatory evolution model is the intensity of selec- tion Ns against deleterious intermediates. In the follow- ing, we attempt to estimate this parameter for mRNA ...
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Novel, Conserved RNA Secondary Structures in MHV-A59, Bovine Coronavirus (BCoV) and MERS-CoV
... homologous RNA sequences from diverse organisms are aligned based on similarities in their primary ...as possible pairing partners. 15 Developing secondary structure models from these alignments ...
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Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome
... single RNA gene in the sense of a genetic ...conserved structures. On the other hand, it is possible that multiple small ncRNAs with short intervening sequences are combined into a single structural ...
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Reverse Genetics Recovery of Lujo Virus and Role of Virus RNA Secondary Structures in Efficient Virus Growth
... virus RNA genome ...the possible presence of a non- templated 5= pppG on both the S and L genomic segments ...panhandle structures, these sequences indicate that the Lujo virus L segment 5= pppG ...
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New windows into retroviral RNA structures
... Double-stranded RNA could be probed with CV1 enzyme, which tends to cleave only towards the middle of longer, more stable helices; and so more often, double-stranded regions were detected by the absence of ...
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Ensemble of Secondary Structures for Encapsidated Satellite Tobacco Mosaic Virus RNA Consistent with Chemical Probing and Crystallography Constraints
... all possible helices that are consistent with chemical modifi- cation and crystallographic data is then assembled into a secondary struc- ture containing 30 helices using a dynamic programming algorithm ...
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Designing RNA secondary structures is hard
... An RNA sequence is a word over an alphabet on four elements {A, C, G, U } called ...bases. RNA sequences fold into secondary structures where some bases match one another while others remain ...
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RNA Movies 2: sequential animation of RNA secondary structures
... ABSTRACT RNA Movies is a simple, yet powerful visualization tool in likeness to a media player application, which enables to browse sequential paths through RNA secondary structure ...of RNA, ...
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RNA Secondary Structures: Combinatorial Models and Folding Algorithms
... than RNA to the general public, as it encodes the essential genetic information for all cells, is standard material in most high school biology classes, and has even made its way into common parlance, such as “it ...
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A novel approach to represent and compare RNA secondary structures
... align RNA structures As stated before, the substitution frequencies in MBR cap- ture the type and amount of structural variation that struc- turally similar, homologous and /or functionally related RNAs can ...
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A method for aligning RNA secondary structures and its application to RNA motif detection
... Vienna RNA package's RNAsubopt function with setting "-e 0", we then folded all obtained sequences to form the structure ...given RNA sequence, the setting "-e 0" resulted in multiple ...
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Web-Beagle: a web server for the alignment of RNA secondary structures
... of RNA secondary ...for RNA secondary structure and a substi- tution matrix of RNA structural elements to perform RNA structural ...of RNA sequences and structures ...
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Comparative Sequence Analysis and Patterns of Covariation in RNA Secondary Structures
... homologous RNA-encoding ...final structures of all five ...final secondary structure model the case of SSU rRNA (the longest of the five RNAs) that maximizes total ...
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Computational Methods for Comparative Non-coding RNA Analysis: from Secondary Structures to Tertiary Structures
... of RNA 3D structural alignment tools relies on the comparison of base pairing interactions in the ...one RNA, which may imply interactions such as base pairs, tertiary interlinks and stacking ...an ...
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A specific orientation of RNA secondary structures is required for initiation of reverse transcription.
... tRNATrP and the U5 sequences lying between the stem structures is necessary for efficient initiation of reverse tran- scription by avian sarcoma/leukosis virus reverse transcriptase (RT)[r] ...
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Sizes of Long RNA Molecules Are Determined by the Branching Patterns of Their Secondary Structures
... Long RNA molecules are at the core of gene regulation across all kingdoms of life, while also serving as genomes in RNA ...ramified secondary structures and are better described as branched ...
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