id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-329102-2y49kcwu	Lan, Tammy C. T.	Structure of the full SARS-CoV-2 RNA genome in infected cells	2020-06-30		.txt	text/plain	9315	507	61	We evaluated the robustness of our in-cell data derived genome-wide model by varying two critical RNA folding parameters used by RNAstructure: 1) the maximum allowed distance for base pairing and 2) the threshold for DMS signal normalization. Previous studies that computationally predicted genome-wide SARS-Cov-2 RNA structures used 1) RNAz, a thermodynamic-based model that additionally takes sequence alignment and considers base pairing conservation (Gruber et al., 2010; Rangan, Zheludev and Das, 2020) , and 2) Contrafold, which predicts RNA secondary structures without physics-based models and instead uses learned parameters based on known structures (Do, Woods and Batzoglou, 2006) . Interestingly, in silico predictions of the RNA structure of the SARS-CoV-2 genome using RNAz (Rangan, Zheludev and Das, 2020) and ScanFold (Andrews et al., 2020) do not find the 3-stem pseudoknot but instead support our in-cell model of Alternative Stem 1.	./cache/cord-329102-2y49kcwu.txt	./txt/cord-329102-2y49kcwu.txt