Fig. 4.

Comparison of base-pair accuracy. Accuracy is the average probability of all base pairs in a single structure over the whole ensemble of possible structures. This structure is the reference structure in this case. We expect good SHAPE data to support the reference structure. In this test ShaKer performs significantly better than the thermodynamic model alone. The experimental data outperform both, which is a testament to its quality. Given the reference structure Sükösd et al. and ShaKer perform even better than SHAPE data which is not surprising since we evaluated for exactly that reference structure. ShaKer performs slightly better than Sükösd et al.