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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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ATTfold: RNA Secondary Structure Prediction With Pseudoknots Based on Attention Mechanism
Frontiers in Genetics, 2020 Accurate RNA secondary structure information is the cornerstone of gene function research and RNA tertiary structure prediction. However, most traditional RNA secondary structure prediction algorithms are based on the dynamic programming (DP) algorithm ...
Yili Wang +14 more
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RNA Locally Optimal Secondary Structures [PDF]
Journal of Computational Biology, 2012 RNA locally optimal secondary structures provide a concise and exhaustive description of all possible secondary structures of a given RNA sequence, and hence a very good representation of the RNA folding space. In this paper, we present an efficient algorithm that computes all locally optimal secondary structures for any folding model that takes into ...
Saffarian, Azadeh +3 more
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