CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNAalifold(seed)		PPfold(seed)
MCC	0.610	>	0.155
Average MCC ± 95% Confidence Intervals	0.574 ± 0.265	>	0.084 ± 0.169
Sensitivity	0.473	>	0.047
Positive Predictive Value	0.798	>	0.538
Total TP	71	>	7
Total TN	9759	<	9835
Total FP	22	<	25
Total FP CONTRA	3	>	0
Total FP INCONS	15	>	6
Total FP COMP	4	<	19
Total FN	79	<	143
P-value	0.0

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

Total Scores
MCC	0.610
Average MCC ± 95% Confidence Intervals	0.574 ± 0.265
Sensitivity	0.473
Positive Predictive Value	0.798
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	516	12	0	12	0	18
3RKF_A	Purine links to Rfam database...	0.74	0.67	0.84	16	847	3	1	2	0	8
3SD1_A	THF links to Rfam database...	0.70	0.59	0.85	17	1513	3	2	1	0	12
4A1C_2	5_8S_rRNA links to Rfam database...	0.50	0.25	1.00	5	4511	2	0	0	2	15
4AOB_A	SAM links to Rfam database...	0.85	0.72	1.00	21	1416	2	0	0	2	8
4ENB_A	crcB links to Rfam database...	0.63	0.40	1.00	6	466	0	0	0	0	9
4ENC_A	crcB links to Rfam database...	0.63	0.40	1.00	6	490	0	0	0	0	9

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.