A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs

By Elena Rivas, Jody Clements, Sean R. Eddy. Nature Methods, 2016

355 citations recorded by the source corpus.

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/50b00321b27436b8632e0734e24dbff045b2d6d7

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Citations in the corpus

Power law tails in phylogenetic systems (2018, neutral): “Discussion This paper was motivated by recent advances (9–14, 16, 21) in predicting protein structure and function from the covariation of sequences, a strategy that has been successful for predicting RNA secondary structure for some time (1, 35).”
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families (2017, methodology): “R-scape (15) is a new method for testing whether covariation analysis supports the presence of a conserved RNA secondary structure.”
Applications of sequence coevolution in membrane protein biochemistry (2017, neutral): “Null hypotheses have been used to better evaluate where cut-offs should be made [163,169].”
RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers (2020, background): “…(3dRNA, RNAComposer, DMD [Dokholyan et al. 1998; Ding and Dokholyan 2005; Ding et al. 2008; Proctor et al. 2011; Krokhotin et al. 2015], ModeRNA [Rother et al. 2011], Rosetta FARFAR, MC-Fold), some of them operating as fully-automated servers, while in Round III (Miao et al. 2017) there were…”
Advancing RNA 3D Structure Prediction: Exploring Hierarchical and Hybrid Approaches in CASP15 (2023, methodology): “25 Next, we retrieved the conserved 2D structure for this RNA family (mammalian CPEB3 ribozyme) provided by R-scape, 43 which revealed two important pseudoknots PK1 and PK2 shown in This result underscores the crucial role of the folding constraints and highlights the efficacy of Vfold2D-MC in predi”
Rfam 14: expanded coverage of metagenomic, viral and microRNA families (2020, methodology): “The R-scape software analyses covariation support for RNA secondary structure based on multiple sequence alignments (16).”