Author: Ramya Rangan; Ivan N. Zheludev; Rhiju Das
Title: RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses Document date: 2020_3_28
ID: kjeqdse5_16
Snippet: As an orthogonal check for the unstructured intervals predicted using Contrafold 2.0 base-pairing probabilities, we used Vienna's RNAplfold to compute unpaired probabilities for each genome position. In general, we found that RNAplfold predicted lower unpaired probabilities than Contrafold 2.0, with only 10 intervals of length at least 15 nucleotides having at least 0.6 probability of being unpaired, in contrast with the 76 stretches predicted by.....
Document: As an orthogonal check for the unstructured intervals predicted using Contrafold 2.0 base-pairing probabilities, we used Vienna's RNAplfold to compute unpaired probabilities for each genome position. In general, we found that RNAplfold predicted lower unpaired probabilities than Contrafold 2.0, with only 10 intervals of length at least 15 nucleotides having at least 0.6 probability of being unpaired, in contrast with the 76 stretches predicted by Contrafold 2.0. Nevertheless, we found that 9 of the 10 intervals predicted by Vienna's RNAplfold overlap with unpaired intervals predicted from our Contrafold 2.0 analysis (regions listed in Supplementary File 1.)
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