CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNAalifold(seed)		IPknot
MCC	0.635	>	0.587
Average MCC ± 95% Confidence Intervals	0.526 ± 0.123	<	0.559 ± 0.136
Sensitivity	0.475	<	0.489
Positive Predictive Value	0.849	>	0.706
Total TP	541	<	557
Total TN	1196919	>	1196767
Total FP	104	<	266
Total FP CONTRA	8	<	25
Total FP INCONS	88	<	207
Total FP COMP	8	<	34
Total FN	599	>	583
P-value	4.61330405444e-08

Comparison of performance of RNAalifold(seed) and IPknot. 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 IPknot).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for RNAalifold(seed) and IPknot).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAalifold(seed) and IPknot. 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 IPknot).

Total Scores
MCC	0.635
Average MCC ± 95% Confidence Intervals	0.526 ± 0.123
Sensitivity	0.475
Positive Predictive Value	0.849
Nr of predictions	16

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1528	12	0	12	0	20
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.69	0.58	0.83	367	1116322	80	5	71	4	266
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7503	0	0	0	0	33
3J3F_8	5_8S_rRNA links to Rfam database...	0.50	0.25	1.00	9	12237	0	0	0	0	27
3RKF_A	Purine links to Rfam database...	0.63	0.47	0.84	16	2192	3	1	2	0	18
3SD1_A	THF links to Rfam database...	0.58	0.40	0.85	17	3896	3	1	2	0	25
3W1K_J	tRNA-Sec links to Rfam database...	0.71	0.50	1.00	19	4167	0	0	0	0	19
3W3S_B	tRNA-Sec links to Rfam database...	0.67	0.45	1.00	18	4735	1	0	0	1	22
3ZEX_C	5_8S_rRNA links to Rfam database...	0.42	0.17	1.00	9	14187	0	0	0	0	43
4A1C_2	5_8S_rRNA links to Rfam database...	0.39	0.15	1.00	5	11776	2	0	0	2	28
4AOB_A	SAM links to Rfam database...	0.72	0.52	1.00	22	4349	1	0	0	1	20
4ENB_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1269	0	0	0	0	13
4ENC_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1320	0	0	0	0	13
4FRG_B	AdoCbl-variant links to Rfam database...	0.73	0.53	1.00	17	3469	0	0	0	0	15
4FRN_A	AdoCbl-variant links to Rfam database...	0.69	0.53	0.90	19	5130	2	1	1	0	17
4JF2_A	preQ1-II links to Rfam database...	0.59	0.35	1.00	11	2839	0	0	0	0	20

Total Scores
MCC	0.587
Average MCC ± 95% Confidence Intervals	0.559 ± 0.136
Sensitivity	0.489
Positive Predictive Value	0.706
Nr of predictions	16

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.40	0.30	0.55	6	1529	5	1	4	0	14
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.61	0.52	0.72	329	1116306	135	8	122	5	304
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7484	25	2	17	6	33
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.33	0.33	12	12210	37	4	20	13	24
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.61	0.48	0.80	20	3891	5	0	5	0	22
3W1K_J	tRNA-Sec links to Rfam database...	0.87	0.79	0.97	30	4155	1	1	0	0	8
3W3S_B	tRNA-Sec links to Rfam database...	0.85	0.75	0.97	30	4722	2	0	1	1	10
3ZEX_C	5_8S_rRNA links to Rfam database...	0.41	0.21	0.79	11	14182	6	1	2	3	41
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	11755	26	4	17	5	28
4AOB_A	SAM links to Rfam database...	0.42	0.33	0.54	14	4345	13	1	11	1	28
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...	0.52	0.42	0.67	8	1314	4	0	4	0	11
4FRG_B	AdoCbl-variant links to Rfam database...	0.69	0.56	0.86	18	3465	3	1	2	0	14
4FRN_A	AdoCbl-variant links to Rfam database...	0.69	0.56	0.87	20	5128	3	1	2	0	16
4JF2_A	preQ1-II links to Rfam database...	0.84	0.74	0.96	23	2826	1	1	0	0	8

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