CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidHomfold‑LAST		RNAwolf
MCC	0.635	>	0.436
Average MCC ± 95% Confidence Intervals	0.574 ± 0.299	>	0.421 ± 0.185
Sensitivity	0.552	>	0.437
Positive Predictive Value	0.743	>	0.452
Total TP	101	>	80
Total TN	11399	>	11358
Total FP	50	<	114
Total FP CONTRA	10	<	22
Total FP INCONS	25	<	75
Total FP COMP	15	<	17
Total FN	82	<	103
P-value	0.0

Comparison of performance of CentroidHomfold-LAST and RNAwolf. 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 CentroidHomfold‑LAST and RNAwolf).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidHomfold-LAST and RNAwolf. 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 CentroidHomfold‑LAST and RNAwolf).

Total Scores
MCC	0.635
Average MCC ± 95% Confidence Intervals	0.574 ± 0.299
Sensitivity	0.552
Positive Predictive Value	0.743
Nr of predictions	9

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...	-0.03	0.00	0.00	0	517	11	0	11	0	18
3J0L_a	-	-0.01	0.00	0.00	0	408	3	1	2	0	11
3RKF_A	Purine links to Rfam database...	0.86	0.75	1.00	18	848	0	0	0	0	6
3SD1_A	THF links to Rfam database...	0.77	0.66	0.90	19	1512	2	1	1	0	10
3U4M_B	-	0.78	0.73	0.84	16	1257	4	0	3	1	6
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.25	0.24	5	4495	29	8	8	13	15
4AOB_A	SAM links to Rfam database...	0.85	0.72	1.00	21	1416	1	0	0	1	8
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...	0.85	0.73	1.00	11	485	0	0	0	0	4

Total Scores
MCC	0.436
Average MCC ± 95% Confidence Intervals	0.421 ± 0.185
Sensitivity	0.437
Positive Predictive Value	0.452
Nr of predictions	9

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...	0.52	0.50	0.56	9	512	7	0	7	0	9
3J0L_a	-	0.14	0.18	0.14	2	397	13	4	8	1	9
3RKF_A	Purine links to Rfam database...	0.89	0.83	0.95	20	845	1	0	1	0	4
3SD1_A	THF links to Rfam database...	0.58	0.59	0.59	17	1504	12	2	10	0	12
3U4M_B	-	0.50	0.50	0.52	11	1255	12	1	9	2	11
4A1C_2	5_8S_rRNA links to Rfam database...	0.12	0.15	0.10	3	4487	38	12	14	12	17
4AOB_A	SAM links to Rfam database...	0.26	0.24	0.30	7	1414	17	2	14	1	22
4ENB_A	crcB links to Rfam database...	0.45	0.40	0.55	6	461	5	1	4	0	9
4ENC_A	crcB links to Rfam database...	0.34	0.33	0.38	5	483	9	0	8	1	10

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