SHAPE Struct Pyle Track Settings
RNA SHAPE Structure from the Pyle group   (All mRNA and EST tracks)

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 SHAPE Reactivity  SHAPE Reactivity (VeroE6 cells, virus isolate USA-WA1/2020)   Schema 
 Shannon Entropy  Shannon Entropy derived from the in vivo SHAPE constrained Superfold structure prediction   Schema 


This track shows data from Anna Pyle's lab at Yale University describing the RNA secondary structure of the SARS-CoV-2 genome. The authors performed experimental measurements using SHAPE (selective 2-hydroxyl acylation) as well as in-silico analysis.

These data are described in depth in de Cesaris Araujo Tavares et al and Huston, Wan, et al.

Display Conventions and Configuration

Two tracks are available:

SHAPE reactivity: A low SHAPE score (<0.4) indicates that the nucleotide is not accessible (folded between complementary regions - base-paired). A mid (0.4<SHAPE<0.85) or high SHAPE reactivity (>0.85) indicates the nucleotide is flexible (single-stranded). A score of -999 means no data for that nucleotide was recovered experimentally. For visualization purposes the minimum display value has been set to -0.5 and the max has been set to 4.

Full Length Shannon Entropy: A genome-wide Shannon entropy profile derived from base pairing probabilities was computed using SuperFold with in vivo SHAPE reactivity as constraints . A low Shannon entropy (near 0) is evidence for well-determined RNA conformation.

Note that the authors provide further data (including secondary structure predictions) at their github repository.


For Shannon entropy, comSuperFold was used with default settings to predict secondary structure for the full-length SARS-CoV-2 RNA genome.

For SHAPE_reactivity, VeroE6 cells were infected with 105 PFU of SARS133 CoV-2 isolate USA-WA1/2020. See the preprint for further details. wigToBigWig was used to convert wiggles from the author's github repository to bigWig files after filtering out headers.

The Github repository with all raw data files can be found here:


Huston NC, Wan H, Araujo Tavares RC, Wilen C, Pyle AM. Comprehensive in-vivo secondary structure of the SARS-CoV-2 genome reveals novel regulatory motifs and mechanisms. bioRxiv. 2020 Jul 10;. PMID: 32676598; PMC: PMC7359520

Araujo Tavares RC, Mahadeshwar G, Pyle AM. The global and local distribution of RNA structure throughout the SARS-CoV-2 genome. bioRxiv. 2020 Jul 7;. doi: 190660