Prediction of RNA Secondary Structure [PDF]
Proceedings of the National Academy of Sciences, 1971 Calculations of the free energy required to close single-strand loops by formation of a base pair in double-helical nucleic acids are reported. These results can be used to estimate the free energy of particular secondary structures for a given RNA molecule under conditions of high-salt concentration.
C, Delisi, D M, Crothers
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Detection of genome-scale ordered RNA structure (GORS) in genomes of positive-stranded RNA viruses:Implications for virus evolution and host persistence [PDF]
, 2004 Discrete RNA secondary and higher-order structures, typically local in extent, play a fundamental role in RNA virus replication. Using new bioinformatics analysis methods, we have identified genome-scale ordered RNA structure (GORS) in many genera and ...
Evans, David J +6 more
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A Novel Structural Measure Separating Non-Coding RNAs from Genomic Backgrounds
Tsinghua Science and Technology, 2015 RNA secondary structure has become the most exploitable feature for ab initio detection of non-coding RNA (ncRNA) genes from genome sequences. Previous work has used Minimum Free Energy (MFE) based methods developed to identify ncRNAs by measuring ...
Yingfeng Wang +2 more
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Evolutionary Algorithm for RNA Secondary Structure Prediction Based on Simulated SHAPE Data. [PDF]
PLoS ONE, 2016 Non-coding RNAs perform a wide range of functions inside the living cells that are related to their structures. Several algorithms have been proposed to predict RNA secondary structure based on minimum free energy.
Soheila Montaseri +2 more
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Secondary Structure of Subgenomic RNA M of SARS-CoV-2
Viruses, 2022 SARS-CoV-2 belongs to the Coronavirinae family. Like other coronaviruses, SARS-CoV-2 is enveloped and possesses a positive-sense, single-stranded RNA genome of ~30 kb. Genomic RNA is used as the template for replication and transcription.
Marta Soszynska-Jozwiak +5 more
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RNA Movies 2: sequential animation of RNA secondary structures [PDF]
, 2007 Kaiser A, Krüger J, Evers DJ. RNA Movies 2: sequential animation of RNA secondary structures. NUCLEIC ACIDS RESEARCH.
Krüger, Jan +2 more
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RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database
BMC Bioinformatics, 2008 Background The ability to access, search and analyse secondary structures of a large set of known RNA molecules is very important for deriving improved RNA energy models, for evaluating computational predictions of RNA secondary structures and for a ...
Andronescu Mirela +3 more
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Widespread selection for extremely high and low levels of secondary structure in coding sequences across all domains of life [PDF]
Open Biology, 2019 Codon composition, GC content and local RNA secondary structures can have a profound effect on gene expression, and mutations affecting these parameters, even though they do not alter the protein sequence, are not neutral in terms of selection.
Daniel Gebert +2 more
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The Rainbow Spectrum of RNA Secondary Structures [PDF]
Bulletin of Mathematical Biology, 2018 In this paper we analyze the length-spectrum of rainbows in RNA secondary structures. A rainbow in a secondary structure is a maximal arc with respect to the partial order induced by nesting. We show that there is a significant gap in this length-spectrum.
Li, Thomas J. X., Reidys, Christian M.
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Complete probabilistic analysis of RNA shapes [PDF]
, 2006 Voß B, Giegerich R, Rehmsmeier M. Complete probabilistic analysis of RNA shapes. BMC Biology. 2006;4(1): 5.Background: Soon after the first algorithms for RNA folding became available, it was recognised that the prediction of only one energetically ...
Marc Rehmsmeier +8 more
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