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. 2015 Mar;21(3):333–346. doi: 10.1261/rna.044891.114

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© 2015 Zhong and Zhang; 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 6. — The base-interaction patterns (left panel) and 3D structures (right panel) of (A) a true C-loop motif instance and (B) an unrelated motif instance. RNAMotifScan ranks A below B; however, RNAMotifScanX is capable of correctly ranking A above B. RNAMotifScanX corrects the ranking by considering the stacking interactions and the crossing base pair. In the left panel, conserved base interactions that are uniquely aligned by RNAMotifScanX are highlighted using the cyan boxes. The right panel shows that the lack of these interactions in B leads to significant structural changes of the core nucleotides (colored, with distance measures to highlight the variation between the same-strand stacked nucleotides, i.e., A1005, C1008 in A and A1942, G1944 in B) as well as the entire structure.