CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		MXScarna(20)
MCC	0.665	>	0.586
Average MCC ± 95% Confidence Intervals	0.640 ± 0.167	>	0.566 ± 0.193
Sensitivity	0.519	>	0.474
Positive Predictive Value	0.859	>	0.731
Total TP	140	>	128
Total TN	34860	>	34848
Total FP	29	<	68
Total FP CONTRA	0	<	6
Total FP INCONS	23	<	41
Total FP COMP	6	<	21
Total FN	130	<	142
P-value	0.0

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

Total Scores
MCC	0.665
Average MCC ± 95% Confidence Intervals	0.640 ± 0.167
Sensitivity	0.519
Positive Predictive Value	0.859
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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	0.586
Average MCC ± 95% Confidence Intervals	0.566 ± 0.193
Sensitivity	0.474
Positive Predictive Value	0.731
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.86	0.74	1.00	20	2983	2	0	0	2	7
3RKF_A	Purine links to Rfam database...	0.72	0.53	1.00	18	2193	0	0	0	0	16
3SD1_A	THF links to Rfam database...	0.63	0.55	0.74	23	3885	8	2	6	0	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.15	0.21	5	11757	36	2	17	17	28
4A1C_3	5S_rRNA links to Rfam database...	0.64	0.56	0.75	30	7100	11	2	8	1	24
4AOB_A	SAM links to Rfam database...	0.62	0.55	0.72	23	4339	10	0	9	1	19
4ENB_A	crcB links to Rfam database...	0.26	0.11	0.67	2	1272	1	0	1	0	17
4ENC_A	crcB links to Rfam database...	0.60	0.37	1.00	7	1319	0	0	0	0	12

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