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_38
Snippet: To obtain probabilities that each genome position in SARS-CoV-2 was unpaired, we computed basepairing probability matrices with Contrafold 2.0 18 in windows of 120 nucleotides sliding by 40 nucleotides, and for each genome position, we summed the probabilities of pairing with all potential partners. We then averaged these nucleotide pairing probabilities across all windows that nucleotide was present in. Additionally, RNAplfold 40 was run with wi.....
Document: To obtain probabilities that each genome position in SARS-CoV-2 was unpaired, we computed basepairing probability matrices with Contrafold 2.0 18 in windows of 120 nucleotides sliding by 40 nucleotides, and for each genome position, we summed the probabilities of pairing with all potential partners. We then averaged these nucleotide pairing probabilities across all windows that nucleotide was present in. Additionally, RNAplfold 40 was run with window size 120 nucleotides, producing another set of unpaired probabilities for each position in the genome.
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