CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	TurboFold(seed)		Mastr(20)
MCC	0.484	>	0.443
Average MCC ± 95% Confidence Intervals	0.504 ± 0.156	>	0.331 ± 0.218
Sensitivity	0.393	>	0.245
Positive Predictive Value	0.601	<	0.809
Total TP	143	>	89
Total TN	65727	<	65855
Total FP	131	>	23
Total FP CONTRA	12	>	1
Total FP INCONS	83	>	20
Total FP COMP	36	>	2
Total FN	221	<	275
P-value	1.26497248087e-08

Comparison of performance of TurboFold(seed) and Mastr(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 TurboFold(seed) and Mastr(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 TurboFold(seed) and Mastr(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for TurboFold(seed) and Mastr(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 TurboFold(seed) and Mastr(20)).

Total Scores
MCC	0.484
Average MCC ± 95% Confidence Intervals	0.504 ± 0.156
Sensitivity	0.393
Positive Predictive Value	0.601
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J3E_8	5_8S_rRNA links to Rfam database...	0.17	0.15	0.21	5	7479	28	2	17	9	28
3J3F_8	5_8S_rRNA links to Rfam database...	0.39	0.36	0.42	13	12215	32	2	16	14	23
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...	0.59	0.48	0.74	20	3889	7	1	6	0	22
3ZEX_C	5_8S_rRNA links to Rfam database...	0.39	0.27	0.56	14	14171	14	2	9	3	38
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	0	6	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.15	0.15	0.15	5	11748	37	3	25	9	28
4AOB_A	SAM links to Rfam database...	0.56	0.40	0.77	17	4349	6	1	4	1	25
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10

Total Scores
MCC	0.443
Average MCC ± 95% Confidence Intervals	0.331 ± 0.218
Sensitivity	0.245
Positive Predictive Value	0.809
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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...	0.00	0.00	0.00	0	12246	0	0	0	0	36
3RKF_A	Purine links to Rfam database...	0.70	0.50	1.00	17	2194	0	0	0	0	17
3SD1_A	THF links to Rfam database...	0.61	0.50	0.75	21	3888	7	1	6	0	21
3ZEX_C	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	14196	0	0	0	0	52
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.84	32	7102	7	0	6	1	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11781	0	0	0	0	33
4AOB_A	SAM links to Rfam database...	0.39	0.26	0.58	11	4352	9	0	8	1	31
4ENB_A	crcB links to Rfam database...	0.39	0.16	1.00	3	1272	0	0	0	0	16
4ENC_A	crcB links to Rfam database...	0.51	0.26	1.00	5	1321	0	0	0	0	14

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