CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PETfold_pre2.0(seed)		PknotsRG
MCC	0.680	>	0.569
Average MCC ± 95% Confidence Intervals	0.632 ± 0.134	>	0.617 ± 0.205
Sensitivity	0.551	>	0.496
Positive Predictive Value	0.843	>	0.660
Total TP	140	>	126
Total TN	33612	>	33587
Total FP	34	<	75
Total FP CONTRA	3	<	10
Total FP INCONS	23	<	55
Total FP COMP	8	<	10
Total FN	114	<	128
P-value	0.0

Comparison of performance of PETfold_pre2.0(seed) and PknotsRG. 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 PETfold_pre2.0(seed) and PknotsRG).
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(seed) and PknotsRG. 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 PETfold_pre2.0(seed) and PknotsRG).

Total Scores
MCC	0.680
Average MCC ± 95% Confidence Intervals	0.632 ± 0.134
Sensitivity	0.551
Positive Predictive Value	0.843
Nr of predictions	8

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...	0.40	0.30	0.55	6	1529	5	0	5	0	14
3J16_L	tRNA links to Rfam database...	0.82	0.70	0.95	21	2753	1	0	1	0	9
3UZL_B	tRNA links to Rfam database...	0.72	0.54	0.95	20	3549	2	1	0	1	17
4A1C_3	5S_rRNA links to Rfam database...	0.83	0.70	0.97	38	7101	1	0	1	0	16
4A1C_2	5_8S_rRNA links to Rfam database...	0.57	0.45	0.71	15	11760	12	0	6	6	18
4AOB_A	SAM links to Rfam database...	0.72	0.57	0.92	24	4345	3	0	2	1	18
4ENB_A	crcB links to Rfam database...	0.50	0.42	0.62	8	1262	5	1	4	0	11
4ENC_A	crcB links to Rfam database...	0.50	0.42	0.62	8	1313	5	1	4	0	11

Total Scores
MCC	0.569
Average MCC ± 95% Confidence Intervals	0.617 ± 0.205
Sensitivity	0.496
Positive Predictive Value	0.660
Nr of predictions	8

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...	0.63	0.55	0.73	11	1525	4	1	3	0	9
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3UZL_B	tRNA links to Rfam database...	0.48	0.38	0.61	14	3547	9	0	9	0	23
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	7101	7	1	6	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.13	5	11742	43	5	29	9	28
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.