Benchmark results.
A comparison of three secondary structure prediction algorithms, using shape data from Deigan et al. [15] for the three RNA molecules, yeast aspartyl tRNA (asp-tRNA), hepatitis C virus internal ribosomal entry site (HCV IRES), and the P546 domain from the bI3 group I intron (P546), along with shape data from [26] for three additional RNA molecules, E. coli phenylalanine tRNA (phe-tRNA), E. coli 5S ribosomal RNA (5S rRNA), and F. nucleatum glycine riboswitch (glycine). The benchmark results are tabulated for (A) RNAsc+shape, (B) RNAstructure+shape, and (C) RNAstructure (with no shape data). Sensitivity is abbreviated by sens., positive predictive value is abbreviated by ppv. The average pointwise entropy, Morgan-Higgs structural diversity, and the expected distance of the computed probabilities to the probing data are abreviated by ave ent., str. div., and edist., respectively. Not shown: results for medloop and V. vulnificus adenine riboswitch (1Y26), for which all three methods have optima sensitivity and ppv values of 1.0.