CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	Cylofold		Multilign(20)
MCC	0.604	>	0.583
Average MCC ± 95% Confidence Intervals	0.655 ± 0.141	>	0.576 ± 0.174
Sensitivity	0.514	>	0.475
Positive Predictive Value	0.716	<	0.724
Total TP	222	>	205
Total TN	46091	<	46118
Total FP	94	>	84
Total FP CONTRA	6	<	7
Total FP INCONS	82	>	71
Total FP COMP	6	=	6
Total FN	210	<	227
P-value	6.12267791166e-06

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

Total Scores
MCC	0.604
Average MCC ± 95% Confidence Intervals	0.655 ± 0.141
Sensitivity	0.514
Positive Predictive Value	0.716
Nr of predictions	13

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...	0.97	0.95	1.00	19	971	0	0	0	0	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.10	0.10	0.11	4	5115	32	1	31	0	38
3AMU_B	tRNA links to Rfam database...	0.67	0.59	0.76	16	2982	7	0	5	2	11
3J20_0	tRNA links to Rfam database...	0.66	0.57	0.77	17	2828	6	1	4	1	13
3J20_1	tRNA links to Rfam database...	0.69	0.70	0.70	16	2903	7	2	5	0	7
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.43	0.72	23	7843	11	0	9	2	30
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...	0.62	0.50	0.78	21	3889	6	0	6	0	21
3ZEX_D	5S_rRNA links to Rfam database...	0.58	0.49	0.69	24	6986	11	0	11	0	25
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4
4FRG_B	AdoCbl-variant links to Rfam database...	0.81	0.66	1.00	21	3465	0	0	0	0	11

Total Scores
MCC	0.583
Average MCC ± 95% Confidence Intervals	0.576 ± 0.174
Sensitivity	0.475
Positive Predictive Value	0.724
Nr of predictions	13

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...	0.97	0.95	1.00	19	971	0	0	0	0	1
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5139	12	1	11	0	42
3AMU_B	tRNA links to Rfam database...	0.63	0.56	0.71	15	2982	8	0	6	2	12
3J20_0	tRNA links to Rfam database...	0.61	0.53	0.70	16	2827	8	1	6	1	14
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
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
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.