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. 2014 Jun;20(6):846–854. doi: 10.1261/rna.043323.113

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© 2014 Rice et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society

This article is distributed exclusively by the RNA Society for the first 12 months after the full-issue publication date (see http://rnajournal.cshlp.org/site/misc/terms.xhtml). After 12 months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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FIGURE 3. — Representative secondary structure modeling for the 5S rRNA without and with SHAPE data. Base pair predictions are illustrated with colored lines (green, purple, and red denoting correct, incorrect, and missing base pairs, respectively) on conventional secondary structure representations (top) and circle plots (bottom). Nucleotides are colored according to their SHAPE reactivity on a black, yellow, red scale for low, medium, and strong reactivity. Nucleotides showing strong preferential reactivity with NMIA (>0.3 units) are indicated with a Δ symbol.