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. 2015 Jun 29;43(15):7504–7520. doi: 10.1093/nar/gkv651

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© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 1. — (A) Structure of the exemplar instance HL_3RG4_004 of motif group HL_72498.12, with annotations used to generate the SCFG/MRF model. The annotations include two basepairs, G53/C61 cWW U54/A58 tWH, bulged bases 59 and 60, and a 3-nucleotide hairpin with sequence UCA in which U55 makes a 5BPh base-phosphate interaction with A58. (B) Corresponding model tree of the SCFG/MRF model. The model tree consists of an Initial node (I₁) to model nucleotides before G53 or after C61, basepair nodes (B₂ and B₃) to generate the paired nucleotides, and a hairpin node (H₄). The nodes are labeled with information about the base combinations observed in the motif exemplar.