CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	TurboFold(seed)		Carnac(20)
MCC	0.565	>	0.493
Average MCC ± 95% Confidence Intervals	0.600 ± 0.172	>	0.351 ± 0.232
Sensitivity	0.454	>	0.286
Positive Predictive Value	0.708	<	0.857
Total TP	143	>	90
Total TN	47004	<	47101
Total FP	72	>	17
Total FP CONTRA	8	>	2
Total FP INCONS	51	>	13
Total FP COMP	13	>	2
Total FN	172	<	225
P-value	0.0

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

Total Scores
MCC	0.565
Average MCC ± 95% Confidence Intervals	0.600 ± 0.172
Sensitivity	0.454
Positive Predictive Value	0.708
Nr of predictions	9

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...	0.92	0.90	0.95	18	971	1	0	1	0	2
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	0.493
Average MCC ± 95% Confidence Intervals	0.351 ± 0.232
Sensitivity	0.286
Positive Predictive Value	0.857
Nr of predictions	9

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...	0.00	0.00	0.00	0	990	0	0	0	0	20
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...	0.60	0.38	0.94	16	3899	1	0	1	0	26
3ZEX_C	5_8S_rRNA links to Rfam database...	0.31	0.13	0.70	7	14186	3	1	2	0	45
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.52	0.88	28	7108	4	0	4	0	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.15	0.71	5	11774	3	0	2	1	28
4AOB_A	SAM links to Rfam database...	0.49	0.33	0.74	14	4352	6	1	4	1	28
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1275	0	0	0	0	19
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1326	0	0	0	0	19

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