CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		HotKnots
MCC	0.601	>	0.509
Average MCC ± 95% Confidence Intervals	0.543 ± 0.159	>	0.486 ± 0.166
Sensitivity	0.483	>	0.460
Positive Predictive Value	0.754	>	0.570
Total TP	193	>	184
Total TN	51821	>	51754
Total FP	81	<	155
Total FP CONTRA	5	<	18
Total FP INCONS	58	<	121
Total FP COMP	18	>	16
Total FN	207	<	216
P-value	2.20167918023e-08

Comparison of performance of ContextFold and HotKnots. 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 ContextFold and HotKnots).
Comparison of average Matthews Correlation Coefficients (MCCs) for ContextFold and HotKnots. 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 ContextFold and HotKnots).

Total Scores
MCC	0.601
Average MCC ± 95% Confidence Intervals	0.543 ± 0.159
Sensitivity	0.483
Positive Predictive Value	0.754
Nr of predictions	14

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.55	0.50	0.63	10	1524	6	0	6	0	10
2LKR_A	-	0.65	0.56	0.76	22	6076	9	0	7	2	17
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J0L_2	-	0.64	0.61	0.69	20	6187	11	2	7	2	13
3J0L_g	-	-0.01	0.00	0.00	0	462	3	1	2	0	4
3J0L_a	-	0.71	0.56	0.90	9	1118	1	0	1	0	7
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3U4M_B	-	0.75	0.57	1.00	21	3139	0	0	0	0	16
3UZL_B	tRNA links to Rfam database...	0.72	0.54	0.95	20	3549	1	0	1	0	17
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.15	0.28	5	11763	26	0	13	13	28
4A1C_3	5S_rRNA links to Rfam database...	0.78	0.63	0.97	34	7105	1	0	1	0	20
4AOB_A	SAM links to Rfam database...	0.52	0.40	0.68	17	4346	9	1	7	1	25
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10

Total Scores
MCC	0.509
Average MCC ± 95% Confidence Intervals	0.486 ± 0.166
Sensitivity	0.460
Positive Predictive Value	0.570
Nr of predictions	14

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.61	0.55	0.69	11	1524	5	0	5	0	9
2LKR_A	-	0.93	0.87	1.00	34	6071	3	0	0	3	5
3J0L_7	-	0.28	0.29	0.29	5	1208	12	0	12	0	12
3J0L_2	-	0.28	0.27	0.29	9	6185	23	3	19	1	24
3J0L_g	-	-0.01	0.00	0.00	0	460	5	1	4	0	4
3J0L_a	-	0.51	0.50	0.53	8	1113	7	3	4	0	8
3J16_L	tRNA links to Rfam database...	0.26	0.23	0.30	7	2752	16	1	15	0	23
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3UZL_B	tRNA links to Rfam database...	0.48	0.38	0.61	14	3547	9	0	9	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.14	5	11745	42	6	25	11	28
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	7101	7	1	6	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...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4

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