CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		RNAalifold(seed)
MCC	0.709	>	0.687
Average MCC ± 95% Confidence Intervals	0.679 ± 0.193	>	0.659 ± 0.107
Sensitivity	0.627	>	0.520
Positive Predictive Value	0.810	<	0.918
Total TP	94	>	78
Total TN	9561	<	9592
Total FP	28	>	12
Total FP CONTRA	3	=	3
Total FP INCONS	19	>	4
Total FP COMP	6	>	5
Total FN	56	<	72
P-value	0.0

Comparison of performance of PPfold(20) and RNAalifold(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 PPfold(20) and RNAalifold(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for PPfold(20) and RNAalifold(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 PPfold(20) and RNAalifold(seed)).

Total Scores
MCC	0.709
Average MCC ± 95% Confidence Intervals	0.679 ± 0.193
Sensitivity	0.627
Positive Predictive Value	0.810
Nr of predictions	7

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.66	0.50	0.90	9	347	1	0	1	0	9
3RKF_A	Purine links to Rfam database...	0.86	0.79	0.95	19	846	1	0	1	0	5
3SD1_A	THF links to Rfam database...	0.81	0.76	0.88	22	1508	3	2	1	0	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.27	0.25	0.29	5	4499	16	1	11	4	15
4AOB_A	SAM links to Rfam database...	0.87	0.83	0.92	24	1411	4	0	2	2	5
4ENB_A	crcB links to Rfam database...	0.63	0.47	0.88	7	464	1	0	1	0	8
4ENC_A	crcB links to Rfam database...	0.64	0.53	0.80	8	486	2	0	2	0	7

Total Scores
MCC	0.687
Average MCC ± 95% Confidence Intervals	0.659 ± 0.107
Sensitivity	0.520
Positive Predictive Value	0.918
Nr of predictions	7

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.57	0.39	0.88	7	349	2	0	1	1	11
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

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