CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ProbKnot		PPfold(seed)
MCC	0.514	>	0.155
Average MCC ± 95% Confidence Intervals	0.515 ± 0.306	>	0.084 ± 0.169
Sensitivity	0.540	>	0.047
Positive Predictive Value	0.503	<	0.538
Total TP	81	>	7
Total TN	9687	<	9835
Total FP	97	>	25
Total FP CONTRA	29	>	0
Total FP INCONS	51	>	6
Total FP COMP	17	<	19
Total FN	69	<	143
P-value	0.0

Comparison of performance of ProbKnot and PPfold(seed). 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 ProbKnot and PPfold(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for ProbKnot and PPfold(seed). 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 ProbKnot and PPfold(seed)).

Total Scores
MCC	0.514
Average MCC ± 95% Confidence Intervals	0.515 ± 0.306
Sensitivity	0.540
Positive Predictive Value	0.503
Nr of predictions	7

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
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
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

Total Scores
MCC	0.155
Average MCC ± 95% Confidence Intervals	0.084 ± 0.169
Sensitivity	0.047
Positive Predictive Value	0.538
Nr of predictions	7

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...	0.49	0.33	0.75	6	520	2	0	2	0	12
3RKF_A	Purine links to Rfam database...	0.00	0.00	0.00	0	866	0	0	0	0	24
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	1533	0	0	0	0	29
4A1C_2	5_8S_rRNA links to Rfam database...	0.10	0.05	0.20	1	4511	23	0	4	19	19
4AOB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	1437	0	0	0	0	29
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	472	0	0	0	0	15
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	496	0	0	0	0	15

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