CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	CRWrnafold		RSpredict(seed)
MCC	0.647	>	0.126
Average MCC ± 95% Confidence Intervals	0.646 ± 0.263	>	0.116 ± 0.143
Sensitivity	0.655	>	0.059
Positive Predictive Value	0.649	>	0.293
Total TP	133	>	12
Total TN	13856	<	14020
Total FP	98	>	30
Total FP CONTRA	21	>	4
Total FP INCONS	51	>	25
Total FP COMP	26	>	1
Total FN	70	<	191
P-value	0.0

Comparison of performance of CRWrnafold and RSpredict(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 CRWrnafold and RSpredict(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for CRWrnafold and RSpredict(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 CRWrnafold and RSpredict(seed)).

Total Scores
MCC	0.647
Average MCC ± 95% Confidence Intervals	0.646 ± 0.263
Sensitivity	0.655
Positive Predictive Value	0.649
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
3AMU_B	tRNA links to Rfam database...	0.77	0.79	0.75	15	1137	8	0	5	3	4
3J16_L	tRNA links to Rfam database...	1.00	1.00	1.00	21	1138	0	0	0	0	0
3SD1_A	THF links to Rfam database...	0.63	0.66	0.61	19	1502	12	6	6	0	10
4A1C_3	5S_rRNA links to Rfam database...	0.85	0.84	0.86	31	2727	7	0	5	2	6
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	44	8	20	16	15
4AOB_A	SAM links to Rfam database...	0.71	0.69	0.74	20	1410	8	4	3	1	9
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	2	0	0	2	4

Total Scores
MCC	0.126
Average MCC ± 95% Confidence Intervals	0.116 ± 0.143
Sensitivity	0.059
Positive Predictive Value	0.293
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	515	13	0	13	0	18
3AMU_B	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1155	2	0	2	0	19
3J16_L	tRNA links to Rfam database...	0.00	0.00	0.00	0	1158	1	0	1	0	21
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	1533	0	0	0	0	29
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2759	4	2	2	0	37
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4512	5	2	2	1	20
4AOB_A	SAM links to Rfam database...	0.42	0.21	0.86	6	1430	1	0	1	0	23
4ENB_A	crcB links to Rfam database...	0.34	0.20	0.60	3	467	2	0	2	0	12
4ENC_A	crcB links to Rfam database...	0.34	0.20	0.60	3	491	2	0	2	0	12

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