CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		RSpredict(seed)
MCC	0.663	>	0.299
Average MCC ± 95% Confidence Intervals	0.639 ± 0.144	>	0.247 ± 0.207
Sensitivity	0.514	>	0.138
Positive Predictive Value	0.861	>	0.656
Total TP	149	>	40
Total TN	35840	<	35952
Total FP	30	>	22
Total FP CONTRA	0	<	2
Total FP INCONS	24	>	19
Total FP COMP	6	>	1
Total FN	141	<	250
P-value	0.0

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

Total Scores
MCC	0.663
Average MCC ± 95% Confidence Intervals	0.639 ± 0.144
Sensitivity	0.514
Positive Predictive Value	0.861
Nr of predictions	9

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...	0.63	0.45	0.90	9	980	1	0	1	0	11
3AMU_B	tRNA links to Rfam database...	0.86	0.74	1.00	20	2983	1	0	0	1	7
3RKF_A	Purine links to Rfam database...	0.73	0.56	0.95	19	2191	1	0	1	0	15
3SD1_A	THF links to Rfam database...	0.68	0.52	0.88	22	3891	3	0	3	0	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.15	0.29	5	11764	16	0	12	4	28
4A1C_3	5S_rRNA links to Rfam database...	0.77	0.63	0.94	34	7104	2	0	2	0	20
4AOB_A	SAM links to Rfam database...	0.74	0.60	0.93	25	4344	3	0	2	1	17
4ENB_A	crcB links to Rfam database...	0.56	0.37	0.88	7	1267	1	0	1	0	12
4ENC_A	crcB links to Rfam database...	0.58	0.42	0.80	8	1316	2	0	2	0	11

Total Scores
MCC	0.299
Average MCC ± 95% Confidence Intervals	0.247 ± 0.207
Sensitivity	0.138
Positive Predictive Value	0.656
Nr of predictions	9

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	0.50	0.67	10	975	5	0	5	0	10
3AMU_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	3001	2	0	2	0	27
3RKF_A	Purine links to Rfam database...	0.71	0.53	0.95	18	2192	1	0	1	0	16
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	3916	0	0	0	0	42
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11777	5	1	3	1	33
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7136	4	1	3	0	54
4AOB_A	SAM links to Rfam database...	0.35	0.14	0.86	6	4364	1	0	1	0	36
4ENB_A	crcB links to Rfam database...	0.30	0.16	0.60	3	1270	2	0	2	0	16
4ENC_A	crcB links to Rfam database...	0.30	0.16	0.60	3	1321	2	0	2	0	16

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