CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	TurboFold(seed)		RNASLOpt
MCC	0.576	>	0.462
Average MCC ± 95% Confidence Intervals	0.559 ± 0.266	>	0.498 ± 0.216
Sensitivity	0.545	>	0.445
Positive Predictive Value	0.619	>	0.491
Total TP	104	>	85
Total TN	17266	>	17261
Total FP	83	<	112
Total FP CONTRA	18	<	31
Total FP INCONS	46	<	57
Total FP COMP	19	<	24
Total FN	87	<	106
P-value	0.0

Comparison of performance of TurboFold(seed) and RNASLOpt. 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 TurboFold(seed) and RNASLOpt).
Comparison of performance of TurboFold(seed) and RNASLOpt. 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 TurboFold(seed) and RNASLOpt).
Comparison of average Matthews Correlation Coefficients (MCCs) for TurboFold(seed) and RNASLOpt. 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 TurboFold(seed) and RNASLOpt).
Comparison of average Matthews Correlation Coefficients (MCCs) for TurboFold(seed) and RNASLOpt. 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 TurboFold(seed) and RNASLOpt).

Total Scores
MCC	0.576
Average MCC ± 95% Confidence Intervals	0.559 ± 0.266
Sensitivity	0.545
Positive Predictive Value	0.619
Nr of predictions	8

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...	-0.03	0.00	0.00	0	513	15	3	12	0	18
3ZEX_C	5_8S_rRNA links to Rfam database...	0.49	0.45	0.54	13	5350	15	2	9	4	16
4A1C_3	5S_rRNA links to Rfam database...	0.86	0.84	0.89	31	2728	6	0	4	2	6
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.25	0.17	5	4486	37	9	16	12	15
4AOB_A	SAM links to Rfam database...	0.67	0.59	0.77	17	1415	6	2	3	1	12
4ENB_A	crcB links to Rfam database...	0.77	0.60	1.00	9	463	0	0	0	0	6
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6
4FRN_A	AdoCbl-variant links to Rfam database...	0.79	0.71	0.87	20	1825	3	1	2	0	8

Total Scores
MCC	0.462
Average MCC ± 95% Confidence Intervals	0.498 ± 0.216
Sensitivity	0.445
Positive Predictive Value	0.491
Nr of predictions	8

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...	0.48	0.39	0.64	7	517	4	0	4	0	11
3ZEX_C	5_8S_rRNA links to Rfam database...	0.32	0.34	0.31	10	5342	36	8	14	14	19
4A1C_3	5S_rRNA links to Rfam database...	0.79	0.73	0.87	27	2732	5	0	4	1	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.30	0.40	0.24	8	4482	35	13	13	9	12
4AOB_A	SAM links to Rfam database...	0.31	0.28	0.38	8	1416	13	3	10	0	21
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...	0.73	0.60	0.90	9	486	1	1	0	0	6
4FRN_A	AdoCbl-variant links to Rfam database...	0.19	0.18	0.22	5	1825	18	6	12	0	23

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