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Pseudoknots in RNA secondary structures
Proceedings of the fourth annual international conference on Computational molecular biology, 2000 <p>RNA molecules are sequences of nucleotides that serve as more than mere intermediaries between DNA and proteins, e.g. as catalytic molecules. Computational prediction of RNA secondary structure is among the few structure prediction problems that can be solved satisfactorily in polynomial time. Most work has been done to predict structures that
Rune B. Lyngsø +1 more
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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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Plant Direct, 2020 After transcription, a messenger RNA (mRNA) is further post‐transcriptionally regulated by several features including RNA secondary structure and covalent RNA modifications (specifically N6‐methyladenosine, m6A). Both RNA secondary structure and m6A have
Marianne C. Kramer +8 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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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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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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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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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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RNAmute: RNA secondary structure mutation analysis tool
BMC Bioinformatics, 2006 Background RNAMute is an interactive Java application that calculates the secondary structure of all single point mutations, given an RNA sequence, and organizes them into categories according to their similarity with respect to the wild type predicted ...
Barash Danny, Churkin Alexander
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Secondary structure prediction for RNA sequences including N6-methyladenosine
Nature Communications, 2022 RNA folding free energy nearest neighbor parameters were determined for sequences with the nucleotide m6A. The RNAstructure software package can accommodate modified nucleotides, enabling secondary structure prediction of sequences with m6A.
Elzbieta Kierzek +6 more
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