CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		IPknot
MCC	0.596	>	0.590
Average MCC ± 95% Confidence Intervals	0.581 ± 0.145	>	0.577 ± 0.120
Sensitivity	0.588	>	0.551
Positive Predictive Value	0.604	<	0.633
Total TP	686	>	643
Total TN	875970	<	876090
Total FP	562	>	493
Total FP CONTRA	127	>	90
Total FP INCONS	322	>	282
Total FP COMP	113	<	121
Total FN	481	<	524
P-value	0.00498321506716

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

Total Scores
MCC	0.596
Average MCC ± 95% Confidence Intervals	0.581 ± 0.145
Sensitivity	0.588
Positive Predictive Value	0.604
Nr of predictions	22

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...	0.58	0.56	0.63	10	512	6	0	6	0	8
2M58_A	-	-0.02	0.00	0.00	0	530	14	3	11	0	12
3J0L_a	-	0.80	0.73	0.89	8	402	2	0	1	1	3
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	2	1	0	1	1
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.89	0.88	0.89	362	421963	88	15	28	45	50
3J3D_C	tRNA links to Rfam database...	0.79	0.79	0.79	15	949	4	3	1	0	4
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2722	29	12	8	9	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.36	0.42	0.31	8	4735	32	9	9	14	11
3U4M_B	-	0.98	0.95	1.00	21	1255	0	0	0	0	1
3W1K_J	tRNA-Sec links to Rfam database...	0.90	0.87	0.93	27	1649	2	1	1	0	4
3W3S_B	tRNA-Sec links to Rfam database...	0.87	0.85	0.90	28	1958	4	0	3	1	5
3ZEX_B	-	0.23	0.23	0.23	81	420993	296	62	216	18	265
3ZEX_C	5_8S_rRNA links to Rfam database...	0.44	0.41	0.48	12	5349	23	4	9	10	17
4A1C_2	5_8S_rRNA links to Rfam database...	0.26	0.25	0.28	5	4498	26	3	10	13	15
4AOB_A	SAM links to Rfam database...	0.62	0.59	0.68	17	1412	9	2	6	1	12
4ATO_G	-	-0.02	0.00	0.00	0	218	2	1	1	0	7
4ENB_A	crcB links to Rfam database...	0.77	0.60	1.00	9	463	0	0	0	0	6
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.77	0.71	0.85	17	1182	3	2	1	0	7
4FRN_A	AdoCbl-variant links to Rfam database...	0.42	0.39	0.46	11	1824	13	6	7	0	17
4JF2_A	preQ1-II links to Rfam database...	0.57	0.50	0.67	12	1064	6	2	4	0	12
4JRC_A	-	0.91	0.82	1.00	14	608	0	0	0	0	3

Total Scores
MCC	0.590
Average MCC ± 95% Confidence Intervals	0.577 ± 0.120
Sensitivity	0.551
Positive Predictive Value	0.633
Nr of predictions	22

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...	0.41	0.33	0.55	6	517	5	1	4	0	12
2M58_A	-	0.71	0.58	0.88	7	536	1	1	0	0	5
3J0L_a	-	0.16	0.18	0.18	2	400	10	3	6	1	9
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	3	8	1	9
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.75	0.74	0.76	305	421966	159	17	80	62	107
3J3D_C	tRNA links to Rfam database...	0.52	0.53	0.53	10	949	9	3	6	0	9
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2723	25	5	14	6	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.36	0.47	0.28	9	4729	40	11	12	17	10
3U4M_B	-	0.91	0.91	0.91	20	1254	3	2	0	1	2
3W1K_J	tRNA-Sec links to Rfam database...	0.97	0.97	0.97	30	1647	1	1	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.94	0.91	0.97	30	1958	2	0	1	1	3
3ZEX_B	-	0.33	0.27	0.40	95	421115	160	26	116	18	251
3ZEX_C	5_8S_rRNA links to Rfam database...	0.51	0.34	0.77	10	5361	7	1	2	4	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.23	0.25	0.22	5	4493	26	8	10	8	15
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
4ATO_G	-	0.49	0.57	0.44	4	211	6	0	5	1	3
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.59	0.53	0.67	8	484	4	0	4	0	7
4FRG_B	AdoCbl-variant links to Rfam database...	0.75	0.71	0.81	17	1181	4	3	1	0	7
4FRN_A	AdoCbl-variant links to Rfam database...	0.79	0.71	0.87	20	1825	3	1	2	0	8
4JF2_A	preQ1-II links to Rfam database...	0.96	0.96	0.96	23	1058	1	1	0	0	1
4JRC_A	-	0.45	0.29	0.71	5	615	2	0	2	0	12

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