CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RSpredict(20)		PPfold(seed)
MCC	0.586	>	0.031
Average MCC ± 95% Confidence Intervals	0.579 ± 0.190	>	0.012 ± 0.029
Sensitivity	0.521	>	0.005
Positive Predictive Value	0.671	>	0.200
Total TP	98	>	1
Total TN	13094	<	13235
Total FP	58	>	23
Total FP CONTRA	19	>	0
Total FP INCONS	29	>	4
Total FP COMP	10	<	19
Total FN	90	<	187
P-value	0.0

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

Total Scores
MCC	0.586
Average MCC ± 95% Confidence Intervals	0.579 ± 0.190
Sensitivity	0.521
Positive Predictive Value	0.671
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...	0.69	0.53	0.91	10	1146	2	0	1	1	9
3RKF_A	Purine links to Rfam database...	0.91	0.88	0.95	21	844	1	1	0	0	3
3SD1_A	THF links to Rfam database...	0.82	0.86	0.78	25	1501	7	5	2	0	4
4A1C_2	5_8S_rRNA links to Rfam database...	0.25	0.30	0.21	6	4487	30	12	11	7	14
4A1C_3	5S_rRNA links to Rfam database...	0.60	0.49	0.75	18	2739	8	0	6	2	19
4AOB_A	SAM links to Rfam database...	0.33	0.21	0.55	6	1426	5	1	4	0	23
4ENB_A	crcB links to Rfam database...	0.54	0.40	0.75	6	464	2	0	2	0	9
4ENC_A	crcB links to Rfam database...	0.51	0.40	0.67	6	487	3	0	3	0	9

Total Scores
MCC	0.031
Average MCC ± 95% Confidence Intervals	0.012 ± 0.029
Sensitivity	0.005
Positive Predictive Value	0.200
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...	0.00	0.00	0.00	0	1157	0	0	0	0	19
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
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2763	0	0	0	0	37
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.