CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	TurboFold(seed)		RNAsubopt
MCC	0.529	>	0.467
Average MCC ± 95% Confidence Intervals	0.527 ± 0.155	>	0.461 ± 0.154
Sensitivity	0.434	>	0.413
Positive Predictive Value	0.650	>	0.534
Total TP	212	>	202
Total TN	79366	>	79314
Total FP	150	<	223
Total FP CONTRA	16	<	26
Total FP INCONS	98	<	150
Total FP COMP	36	<	47
Total FN	277	<	287
P-value	2.10198558684e-08

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

Total Scores
MCC	0.529
Average MCC ± 95% Confidence Intervals	0.527 ± 0.155
Sensitivity	0.434
Positive Predictive Value	0.650
Nr of predictions	14

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	1525	15	2	13	0	20
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
3W1K_J	tRNA-Sec links to Rfam database...	0.87	0.79	0.97	30	4155	1	1	0	0	8
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
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...	0.78	0.61	1.00	19	2831	0	0	0	0	12

Total Scores
MCC	0.467
Average MCC ± 95% Confidence Intervals	0.461 ± 0.154
Sensitivity	0.413
Positive Predictive Value	0.534
Nr of predictions	14

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	1525	15	2	13	0	20
3J3E_8	5_8S_rRNA links to Rfam database...	0.16	0.15	0.18	5	7475	32	2	21	9	28
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.33	0.32	12	12209	39	4	21	14	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	0.50	0.75	21	3888	7	1	6	0	21
3W1K_J	tRNA-Sec links to Rfam database...	0.87	0.79	0.97	30	4155	1	1	0	0	8
3ZEX_C	5_8S_rRNA links to Rfam database...	0.24	0.21	0.28	11	14157	42	1	27	14	41
4A1C_3	5S_rRNA links to Rfam database...	0.70	0.59	0.82	32	7101	7	1	6	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.14	0.15	0.13	5	11742	43	5	29	9	28
4AOB_A	SAM links to Rfam database...	0.52	0.43	0.64	18	4343	11	2	8	1	24
4ENB_A	crcB links to Rfam database...	0.70	0.58	0.85	11	1262	2	1	1	0	8
4ENC_A	crcB links to Rfam database...	0.32	0.26	0.42	5	1314	7	0	7	0	14
4FRN_A	AdoCbl-variant links to Rfam database...	0.51	0.44	0.59	16	5124	11	3	8	0	20
4JF2_A	preQ1-II links to Rfam database...	0.61	0.52	0.73	16	2828	6	3	3	0	15

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