CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASampler(20)		ProbKnot
MCC	0.659	>	0.630
Average MCC ± 95% Confidence Intervals	0.680 ± 0.147	>	0.628 ± 0.163
Sensitivity	0.563	<	0.664
Positive Predictive Value	0.778	>	0.603
Total TP	189	<	223
Total TN	46495	>	46368
Total FP	90	<	192
Total FP CONTRA	24	<	58
Total FP INCONS	30	<	89
Total FP COMP	36	<	45
Total FN	147	>	113
P-value	9.45186852942e-09

Comparison of performance of RNASampler(20) and ProbKnot. Positive Predictive Value (PPV) is plotted against sensitivity. Each dot represents a single test of each method. See tables below for raw data (individual counts for RNASampler(20) and ProbKnot).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNASampler(20) and ProbKnot. The whiskers correspond to 95% confidence intervals (CIs). 'n' denotes the number of MCCs used to calculate average MCCs and CIs. See tables below for raw data (individual counts for RNASampler(20) and ProbKnot).

Total Scores
MCC	0.659
Average MCC ± 95% Confidence Intervals	0.680 ± 0.147
Sensitivity	0.563
Positive Predictive Value	0.778
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3IZ4_A	tmRNA links to Rfam database...	0.52	0.41	0.65	39	25476	26	15	6	5	56
3NPB_A	SAM links to Rfam database...	0.75	0.57	1.00	21	2257	5	0	0	5	16
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.50	0.52	11	4743	19	5	5	9	11
3PDR_A	ykoK links to Rfam database...	0.84	0.76	0.93	38	4799	5	1	2	2	12
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.81	0.69	0.95	20	1512	1	0	1	0	9
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.25	0.24	5	4495	30	3	13	14	15
4AOB_A	SAM links to Rfam database...	0.70	0.59	0.85	17	1417	4	0	3	1	12
4ENB_A	crcB links to Rfam database...	0.68	0.47	1.00	7	465	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	0	0	0	0	4

Total Scores
MCC	0.630
Average MCC ± 95% Confidence Intervals	0.628 ± 0.163
Sensitivity	0.664
Positive Predictive Value	0.603
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3IZ4_A	tmRNA links to Rfam database...	0.59	0.61	0.57	58	25435	49	17	26	6	37
3NPB_A	SAM links to Rfam database...	0.79	0.73	0.87	27	2247	9	0	4	5	10
3O58_3	5_8S_rRNA links to Rfam database...	0.38	0.50	0.29	11	4726	42	10	17	15	11
3PDR_A	ykoK links to Rfam database...	0.88	0.92	0.85	46	4786	10	5	3	2	4
3RKF_A	Purine links to Rfam database...	0.87	0.83	0.91	20	844	2	2	0	0	4
3SD1_A	THF links to Rfam database...	0.66	0.69	0.65	20	1502	11	6	5	0	9
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.25	0.13	5	4477	49	13	21	15	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	1	1	0	0	4
4ENC_A	crcB links to Rfam database...	0.52	0.53	0.53	8	481	8	0	7	1	7

Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.