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. 2020 Sep 10;8:e9882. doi: 10.7717/peerj.9882

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©2020 Andrews et al.

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

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(A) IGV visualization of results with KSHV genome coordinates followed by ScanFold-Fold predicted base pairs represented as arcs (colored green for bp with average z-score < − 1, yellow for bp with negative average z-scores > − 1, and grey for >0), the genome sequence (A, C, G, and T are in green, blue, orange and red, respectively). (B) The bottom panel contains motif secondary structures predicted by ScanFold-Fold depicted using VARNA (Darty, Denise & Ponty, 2009). The MRE is represented as an orange highlight on the arc diagrams and as orange bps in the secondary structures. The nucleotides from the ENE motif which have been crystalized (Mitton-Fry et al., 2010) are highlighted in green.