SARS-CoV-2 Structure Extracts

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The ScanFold approach defines specific motifs of likely function. All predicted motifs containing at least one base pair with an average Zavg < -1 have been modeled, annotated, and compiled into individual PDF files for easy viewing.

structures_zavg-1.pdf

Additionally, each of these motifs has been queried (using the Incarnato lab's cm-builder script) against ~25K coronavirus genomes using the Eddy lab's 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.

scanfold.cmbuilt.combined.pdf

Results for experimentally informed motifs:

rouskintop10.extracts.-1.pdf

pyletop10.extracts.-1.pdf

incarnatotop10.extracts.-1.pdf

alltop10.-1.extract.pdf

alltop10.infernal_r-scape.combined.pdf

alltop10.infernal_cacofold.combined.pdf

Full cm-builder/Infernal/R-scape/CaCoFold Results:

Full Motif Conservation Results (Download .zip Archive)

 

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