CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ProbKnot		RDfolder
MCC	0.566	>	0.412
Average MCC ± 95% Confidence Intervals	0.520 ± 0.153	>	0.364 ± 0.149
Sensitivity	0.506	>	0.317
Positive Predictive Value	0.643	>	0.549
Total TP	214	>	134
Total TN	35200	<	35289
Total FP	123	>	114
Total FP CONTRA	19	>	9
Total FP INCONS	100	<	101
Total FP COMP	4	=	4
Total FN	209	<	289
P-value	3.33194562506e-08

Comparison of performance of ProbKnot and RDfolder. 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 ProbKnot and RDfolder).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for ProbKnot and RDfolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for ProbKnot and RDfolder. 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 ProbKnot and RDfolder).

Total Scores
MCC	0.566
Average MCC ± 95% Confidence Intervals	0.520 ± 0.153
Sensitivity	0.506
Positive Predictive Value	0.643
Nr of predictions	17

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2LA5_A	-	0.45	0.32	0.67	6	621	3	0	3	0	13
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1525	15	2	13	0	20
2XQD_Y	tRNA links to Rfam database...	0.90	0.81	1.00	22	2828	1	0	0	1	5
3AKZ_H	tRNA links to Rfam database...	0.73	0.75	0.72	21	2672	8	4	4	0	7
3AM1_B	-	0.74	0.71	0.78	25	3208	7	1	6	0	10
3AMU_B	tRNA links to Rfam database...	0.65	0.59	0.73	16	2981	8	0	6	2	11
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J0L_a	-	0.55	0.50	0.62	8	1115	5	2	3	0	8
3J0L_g	-	-0.01	0.00	0.00	0	458	7	2	5	0	4
3J16_L	tRNA links to Rfam database...	0.35	0.33	0.38	10	2749	16	1	15	0	20
3NKB_B	-	0.59	0.54	0.67	14	1995	7	0	7	0	12
3RKF_A	Purine links to Rfam database...	0.73	0.59	0.91	20	2189	2	1	1	0	14
3SD1_A	THF links to Rfam database...	0.55	0.48	0.65	20	3885	11	2	9	0	22
4AOB_A	SAM links to Rfam database...	0.50	0.40	0.63	17	4344	11	2	8	1	25
4ENB_A	crcB links to Rfam database...	0.73	0.58	0.92	11	1263	1	1	0	0	8
4ENC_A	crcB links to Rfam database...	0.45	0.42	0.50	8	1310	8	1	7	0	11

Total Scores
MCC	0.412
Average MCC ± 95% Confidence Intervals	0.364 ± 0.149
Sensitivity	0.317
Positive Predictive Value	0.549
Nr of predictions	17

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KX8_A	7SK links to Rfam database...	0.88	0.78	1.00	14	847	0	0	0	0	4
2LA5_A	-	0.46	0.26	0.83	5	624	1	0	1	0	14
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1526	14	2	12	0	20
2XQD_Y	tRNA links to Rfam database...	0.88	0.78	1.00	21	2829	0	0	0	0	6
3AKZ_H	tRNA links to Rfam database...	0.48	0.43	0.55	12	2679	11	1	9	1	16
3AM1_B	-	0.47	0.43	0.54	15	3212	13	1	12	0	20
3AMU_B	tRNA links to Rfam database...	0.18	0.15	0.22	4	2985	16	2	12	2	23
3J0L_7	-	-0.01	0.00	0.00	0	1220	5	0	5	0	17
3J0L_a	-	-0.01	0.00	0.00	0	1124	4	1	3	0	16
3J0L_g	-	-0.01	0.00	0.00	0	462	3	1	2	0	4
3J16_L	tRNA links to Rfam database...	0.22	0.17	0.31	5	2759	11	0	11	0	25
3NKB_B	-	0.37	0.31	0.47	8	1999	9	0	9	0	18
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.30	0.17	0.54	7	3903	6	0	6	0	35
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ENB_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1265	4	0	4	0	13
4ENC_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1316	4	0	4	0	13

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