CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RDfolder		PPfold(seed)
MCC	0.395	>	0.160
Average MCC ± 95% Confidence Intervals	0.384 ± 0.227	>	0.061 ± 0.145
Sensitivity	0.347	>	0.035
Positive Predictive Value	0.476	<	0.750
Total TP	59	>	6
Total TN	7524	<	7640
Total FP	68	>	2
Total FP CONTRA	11	>	0
Total FP INCONS	54	>	2
Total FP COMP	3	>	0
Total FN	111	<	164
P-value	0.0

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

Total Scores
MCC	0.395
Average MCC ± 95% Confidence Intervals	0.384 ± 0.227
Sensitivity	0.347
Positive Predictive Value	0.476
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...	-0.03	0.00	0.00	0	514	14	3	11	0	18
3AMU_B	tRNA links to Rfam database...	0.20	0.21	0.22	4	1139	16	4	10	2	15
3J16_L	tRNA links to Rfam database...	0.26	0.24	0.31	5	1143	11	0	11	0	16
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
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

Total Scores
MCC	0.160
Average MCC ± 95% Confidence Intervals	0.061 ± 0.145
Sensitivity	0.035
Positive Predictive Value	0.750
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...	0.49	0.33	0.75	6	520	2	0	2	0	12
3AMU_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	1157	0	0	0	0	19
3J16_L	tRNA links to Rfam database...	0.00	0.00	0.00	0	1159	0	0	0	0	21
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
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.