CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidHomfold‑LAST		ProbKnot
MCC	0.635	>	0.527
Average MCC ± 95% Confidence Intervals	0.574 ± 0.299	>	0.532 ± 0.222
Sensitivity	0.552	=	0.552
Positive Predictive Value	0.743	>	0.518
Total TP	101	=	101
Total TN	11399	>	11340
Total FP	50	<	112
Total FP CONTRA	10	<	35
Total FP INCONS	25	<	59
Total FP COMP	15	<	18
Total FN	82	=	82
P-value	0.0

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

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	0.527
Average MCC ± 95% Confidence Intervals	0.532 ± 0.222
Sensitivity	0.552
Positive Predictive Value	0.518
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	513	15	3	12	0	18
3J0L_a	-	0.60	0.64	0.58	7	399	6	4	1	1	4
3RKF_A	Purine links to Rfam database...	0.87	0.83	0.91	20	844	2	2	0	0	4
3SD1_A	THF links to Rfam database...	0.66	0.69	0.65	20	1502	11	6	5	0	9
3U4M_B	-	0.58	0.59	0.59	13	1254	9	2	7	0	9
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.25	0.13	5	4477	49	13	21	15	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	1	1	0	0	4
4ENC_A	crcB links to Rfam database...	0.52	0.53	0.53	8	481	8	0	7	1	7

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