Author: Jacob Kames; David Dillon Holcomb; Ofer Kimchi; Michael DiCuccio; Nobuko Hamasaki-Katagiri; Tony Wang; Anton A Komar; Aikaterini Alexaki; Chava Kimchi-Sarfaty
Title: Sequence analysis of SARS-CoV-2 genome reveals features important for vaccine design Document date: 2020_3_31
ID: 2fn25l6m_38
Snippet: To ensure our results are robust to the prediction algorithm chosen as well as to the size of the window examined, we used two secondary structure prediction algorithms on two window sizes. We used NuPack to predict the minimum free energy (MFE) secondary structure on the 100 nucleotides (nts) following the frameshift, and our own recently published free energy landscape enumeration algorithm to examine the full structure landscape of the 75 nts .....
Document: To ensure our results are robust to the prediction algorithm chosen as well as to the size of the window examined, we used two secondary structure prediction algorithms on two window sizes. We used NuPack to predict the minimum free energy (MFE) secondary structure on the 100 nucleotides (nts) following the frameshift, and our own recently published free energy landscape enumeration algorithm to examine the full structure landscape of the 75 nts following the frameshift [28, 29] . For the latter, we employed the heuristic that the minimum stem length was set to 4. Aside from this heuristic, the two algorithms differ primarily in the loop entropy calculation, which especially affects the probability of pseudoknot formation.
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