Dataset S3 - Motif Conservation Analyses

Downloadable File
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: 
Time Executed: 
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 (
Default Track?: