CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNAalifold(seed)		CentroidHomfold‑LAST
MCC	0.664	>	0.638
Average MCC ± 95% Confidence Intervals	0.629 ± 0.164	<	0.644 ± 0.222
Sensitivity	0.518	<	0.617
Positive Predictive Value	0.862	>	0.672
Total TP	131	<	156
Total TN	15092	>	15012
Total FP	28	<	92
Total FP CONTRA	4	<	26
Total FP INCONS	17	<	50
Total FP COMP	7	<	16
Total FN	122	>	97
P-value	1.81480685939e-07

Comparison of performance of RNAalifold(seed) 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 RNAalifold(seed) and CentroidHomfold‑LAST).
Comparison of performance of RNAalifold(seed) 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 RNAalifold(seed) and CentroidHomfold‑LAST).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAalifold(seed) 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 RNAalifold(seed) and CentroidHomfold‑LAST).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAalifold(seed) 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 RNAalifold(seed) and CentroidHomfold‑LAST).

Total Scores
MCC	0.664
Average MCC ± 95% Confidence Intervals	0.629 ± 0.164
Sensitivity	0.518
Positive Predictive Value	0.862
Nr of predictions	11

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
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	516	12	0	12	0	18
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
3W3S_B	tRNA-Sec links to Rfam database...	0.71	0.52	1.00	17	1972	2	0	0	2	16
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
4FRG_B	AdoCbl-variant links to Rfam database...	0.84	0.71	1.00	17	1185	0	0	0	0	7
4FRN_A	AdoCbl-variant links to Rfam database...	0.78	0.68	0.90	19	1827	2	1	1	0	9

Total Scores
MCC	0.638
Average MCC ± 95% Confidence Intervals	0.644 ± 0.222
Sensitivity	0.617
Positive Predictive Value	0.672
Nr of predictions	11

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...	0.94	0.94	0.94	17	339	2	0	1	1	1
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	517	11	0	11	0	18
3RKF_A	Purine links to Rfam database...	0.86	0.75	1.00	18	848	0	0	0	0	6
3SD1_A	THF links to Rfam database...	0.77	0.66	0.90	19	1512	2	1	1	0	10
3W3S_B	tRNA-Sec links to Rfam database...	0.94	0.88	1.00	29	1960	1	0	0	1	4
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.25	0.24	5	4495	29	8	8	13	15
4AOB_A	SAM links to Rfam database...	0.85	0.72	1.00	21	1416	1	0	0	1	8
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	0	0	0	0	4
4FRG_B	AdoCbl-variant links to Rfam database...	0.43	0.50	0.40	12	1172	18	6	12	0	12
4FRN_A	AdoCbl-variant links to Rfam database...	0.37	0.46	0.32	13	1807	28	11	17	0	15

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