Downloadable File
Organism:
Betacoronavirus Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
Program, Pipeline Name or Method Name:
Infernal, cmbuild, ScanFold, SHAPE, DMS, R-scape, CaCoFold
Program, Pipeline or Method version:
Infernal, cmbuild, ScanFold, SHAPE, DMS, R-scape, CaCoFold
Source Name:
RNAStructuromeDB
Time Executed:
11/11/2020
Materials & Methods (Description and/or Program Settings):
Each of the motifs from Dataset S2 has been queried (using the Incarnato lab's cm-builder script) against ~25K coronavirus genomes using the Infernal program in order to generate covariation models of the given motif. The resulting covariation model stockholm alignments were then tested using the R-scape program for evidence of statisitcally significant covariation. Here base pairs with significant covariation (GTp test; E < 0.05) are highlighted in green. Additionally, each motif stockholm (Dataset S4) was used to generate a denovo structure model using the CaCoFold algorithm (https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008387).
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