Extended Data Fig. 2: Support from DMS reactivity for in vivo formation of control structures.
From: Comprehensive analysis of Saccharomyces cerevisiae intron structures in vivo
A) PPV, B) sensitivity, and C) F1 score for structure prediction of a set of control RNA structures (rRNAs, tRNAs, snRNAs, and mRNAs; Supplementary Table 2), using RNAstructure guided by DMS with varying helix confidence estimate cutoffs for calling stems. The black dotted line represents the helix confidence estimate 0.7 chosen in this paper. The red dotted line represents the PPV, sensitivity, and F1 score for Vienna RNA structure prediction without using DMS data. D)-E) DMS-MaPseq structure prediction for the U1 snRNA compared to the native secondary structure. D) DMS-guided secondary structure prediction for the U1 snRNA, with reactivity values overlaid and helix confidence estimates indicated in green percentages. E) Native secondary structure for the U1 snRNA, with DMS reactivity overlaid along with helix confidence estimates. For the native structure, helix confidence estimates were computed as the percent of bootstrapping iterations where the helix was recovered when sampling DMS reactivity values and making structure predictions.
