On an enhancement of RNA probing data using information theory

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

RNA	Length	Hajdin et al. [8]			Our method
RNA	Length	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

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

ISSN: 1748-7188