CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	IPknot		Multilign(20)
MCC	0.620	>	0.577
Average MCC ± 95% Confidence Intervals	0.625 ± 0.119	>	0.567 ± 0.146
Sensitivity	0.516	>	0.488
Positive Predictive Value	0.749	>	0.688
Total TP	236	>	223
Total TN	58866	>	58857
Total FP	90	<	111
Total FP CONTRA	7	<	9
Total FP INCONS	72	<	92
Total FP COMP	11	>	10
Total FN	221	<	234
P-value	1.61358433984e-08

Comparison of performance of IPknot and Multilign(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 IPknot and Multilign(20)).
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 IPknot and Multilign(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for IPknot and Multilign(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 IPknot and Multilign(20)).

Total Scores
MCC	0.620
Average MCC ± 95% Confidence Intervals	0.625 ± 0.119
Sensitivity	0.516
Positive Predictive Value	0.749
Nr of predictions	13

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J20_0	tRNA links to Rfam database...	0.45	0.40	0.52	12	2827	12	0	11	1	18
3J2L_3	5S_rRNA links to Rfam database...	0.66	0.55	0.81	29	7839	9	0	7	2	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
3ZEX_D	5S_rRNA links to Rfam database...	0.72	0.63	0.82	31	6983	7	0	7	0	18
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	1	5	0	23
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

Total Scores
MCC	0.577
Average MCC ± 95% Confidence Intervals	0.567 ± 0.146
Sensitivity	0.488
Positive Predictive Value	0.688
Nr of predictions	13

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.63	0.56	0.71	15	2982	8	0	6	2	12
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J20_0	tRNA links to Rfam database...	0.61	0.53	0.70	16	2827	8	1	6	1	14
3J2L_3	5S_rRNA links to Rfam database...	0.65	0.53	0.80	28	7840	9	0	7	2	25
3RKF_A	Purine links to Rfam database...	0.77	0.62	0.95	21	2189	1	0	1	0	13
3SD1_A	THF links to Rfam database...	0.57	0.48	0.69	20	3887	9	1	8	0	22
3ZEX_D	5S_rRNA links to Rfam database...	0.75	0.65	0.86	32	6984	5	1	4	0	17
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.84	32	7102	6	0	6	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.15	0.15	0.15	5	11747	33	3	26	4	28
4AOB_A	SAM links to Rfam database...	0.49	0.38	0.64	16	4346	10	1	8	1	26
4ENB_A	crcB links to Rfam database...	0.34	0.26	0.45	5	1264	6	1	5	0	14
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.12	0.09	0.17	3	3468	15	0	15	0	29

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