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Table 5 Target identification results for 18 test sequences with SHAPE profiles from [8]

From: On an enhancement of RNA probing data using information theory

RNA Length Hajdin et al. [8] Our method
Sens PPV Acc Sens PPV Acc
Pre-Q1 riboswitch, B. subtilis 34 100 100 100 100 100 100
Fluoride riboswitch, P. syringae 66 93.8 93.8 93.8 100 100 100
Adenine riboswitch, V. vulnificus 71 100 100 100 100 100 100
tRNA(asp), yeast 75 95.2 95.2 95.2 100 100 100
tRNA(phe), E. coli 76 100 84.0 91.7 100 100 100
TPP riboswitch, E. coli 79 95.5 87.5 91.4 95.6 100 97.7
SARS corona virus pseudoknot 82 84.6 88.0 86.3 97.4 84.4 90.5
cyclic-di-GMP riboswitch, V. cholerae 97 89.3 86.2 87.7 100 96.6 98.3
5S rRNA, E. coli 120 85.7 76.9 81.2 100 97.3 98.6
M-Box riboswitch, B. subtilis 154 87.5 91.3 89.4 89.7 97.8 93.5
P546 domain, bI3 group I intron 155 94.6 96.4 95.5 98.2 100 99.1
Lysine riboswitch, T. maritima 174 87.3 88.7 88.0 94.8 100 97.3
Group I intron, Azoarcus sp. 214 92.1 95.1 93.6 96.5 96.5 96.5
Hepatitis C virus IRES domain 336 92.3 96.0 94.1 98.0 97.0 97.5
Group II intron, O. iheyensis 412 93.2 97.6 95.4 94.4 100 97.1
Group I Intron, T. thermophila 425 93.9 91.2 92.5 96.8 92.3 94.5
5′ domain of 23S rRNA, E. coli 511 97.2 76.8 86.4 98.7 83.4 90.4
5′ domain of 16S rRNA, E. coli 530 93.0 83.6 88.2 97.6 89.7 93.5
Average   93.0 90.4 91.6 97.6 96.4 96.9
  1. We consider the accepted secondary structure excluding pseudoknots as the target. Our method identifies the distinguished structure from a Boltzmann sample of \(2^{10}\) structures via 10 base-pair queries on the target. For each base-pair query, we consider the error rates of accepting or rejecting a base pair, \(e_0=0.05\) and \(e_1=0.01\). To compare the structure prediction approach in [8] and our method, we present three measures of performance: sensitivities (Sens), the fraction of pairs in the accepted structure that are predicted (\(\text {Sens}=\frac{\text {FP}}{\text {TP}+\text {FN}}\)); positive predictive value (PPV), the proportion of predicted pairs that are in the accepted structure (\(\text {PPV}=\frac{\text {FP}}{\text {TP}+\text {FP}}\)); and accuracy (Acc), the harmonic mean of Sens and PPV (\(\text {Acc}=\frac{2\cdot \text {Sens} \cdot \text {PPV}}{\text {Sens}+\text {PPV}}\)). The average accuracy of both methods is displayed in italics