CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidAlifold(20)		CentroidHomfold‑LAST
MCC	0.691	>	0.631
Average MCC ± 95% Confidence Intervals	0.669 ± 0.151	>	0.655 ± 0.173
Sensitivity	0.515	>	0.496
Positive Predictive Value	0.933	>	0.807
Total TP	139	>	134
Total TN	34874	>	34857
Total FP	15	<	41
Total FP CONTRA	1	<	5
Total FP INCONS	9	<	27
Total FP COMP	5	<	9
Total FN	131	<	136
P-value	0.0

Comparison of performance of CentroidAlifold(20) and CentroidHomfold-LAST. 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 CentroidAlifold(20) and CentroidHomfold‑LAST).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidAlifold(20) and CentroidHomfold-LAST. 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 CentroidAlifold(20) and CentroidHomfold‑LAST).

Total Scores
MCC	0.691
Average MCC ± 95% Confidence Intervals	0.669 ± 0.151
Sensitivity	0.515
Positive Predictive Value	0.933
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...	0.72	0.53	1.00	18	2193	0	0	0	0	16
3SD1_A	THF links to Rfam database...	0.71	0.52	0.96	22	3893	1	0	1	0	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.26	0.15	0.45	5	11770	8	1	5	2	28
4A1C_3	5S_rRNA links to Rfam database...	0.76	0.63	0.92	34	7103	4	0	3	1	20
4AOB_A	SAM links to Rfam database...	0.75	0.57	1.00	24	4347	1	0	0	1	18
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.60	0.37	1.00	7	1319	0	0	0	0	12

Total Scores
MCC	0.631
Average MCC ± 95% Confidence Intervals	0.655 ± 0.173
Sensitivity	0.496
Positive Predictive Value	0.807
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...	0.82	0.70	0.95	19	2983	3	0	1	2	8
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...	0.64	0.45	0.90	19	3895	2	0	2	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.18	5	11753	29	5	18	6	28
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.56	0.83	30	7104	6	0	6	0	24
4AOB_A	SAM links to Rfam database...	0.71	0.50	1.00	21	4350	1	0	0	1	21
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1315	0	0	0	0	8

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