CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidHomfold‑LAST		RDfolder
MCC	0.697	>	0.515
Average MCC ± 95% Confidence Intervals	0.645 ± 0.240	>	0.491 ± 0.228
Sensitivity	0.641	>	0.455
Positive Predictive Value	0.771	>	0.603
Total TP	148	>	105
Total TN	10349	<	10367
Total FP	47	<	71
Total FP CONTRA	12	<	16
Total FP INCONS	32	<	53
Total FP COMP	3	>	2
Total FN	83	<	126
P-value	1.34193807955e-08

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

Total Scores
MCC	0.697
Average MCC ± 95% Confidence Intervals	0.645 ± 0.240
Sensitivity	0.641
Positive Predictive Value	0.771
Nr of predictions	11

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
3J20_0	tRNA links to Rfam database...	0.41	0.52	0.34	11	1187	22	7	14	1	10
3J3D_C	tRNA links to Rfam database...	0.73	0.79	0.68	15	946	7	3	4	0	4
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
3W3S_B	tRNA-Sec links to Rfam database...	0.94	0.88	1.00	29	1960	1	0	0	1	4
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
4JRC_A	-	0.87	0.76	1.00	13	609	0	0	0	0	4

Total Scores
MCC	0.515
Average MCC ± 95% Confidence Intervals	0.491 ± 0.228
Sensitivity	0.455
Positive Predictive Value	0.603
Nr of predictions	11

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	514	14	3	11	0	18
3J0L_a	-	-0.02	0.00	0.00	0	407	4	3	1	0	11
3J20_0	tRNA links to Rfam database...	0.82	0.76	0.89	16	1201	3	1	1	1	5
3J3D_C	tRNA links to Rfam database...	0.76	0.79	0.75	15	948	5	3	2	0	4
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...	0.35	0.24	0.54	7	1520	6	1	5	0	22
3W3S_B	tRNA-Sec links to Rfam database...	0.29	0.27	0.33	9	1962	18	2	16	0	24
4AOB_A	SAM links to Rfam database...	0.42	0.38	0.48	11	1414	13	3	9	1	18
4ENB_A	crcB links to Rfam database...	0.48	0.40	0.60	6	462	4	0	4	0	9
4ENC_A	crcB links to Rfam database...	0.48	0.40	0.60	6	486	4	0	4	0	9
4JRC_A	-	0.94	0.88	1.00	15	607	0	0	0	0	2

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