CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	TurboFold(seed)		RNAalifold(20)
MCC	0.712	>	0.694
Average MCC ± 95% Confidence Intervals	0.723 ± 0.195	>	0.658 ± 0.199
Sensitivity	0.684	>	0.631
Positive Predictive Value	0.749	<	0.771
Total TP	128	>	118
Total TN	12269	<	12287
Total FP	59	>	40
Total FP CONTRA	14	>	9
Total FP INCONS	29	>	26
Total FP COMP	16	>	5
Total FN	59	<	69
P-value	0.0

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

Total Scores
MCC	0.712
Average MCC ± 95% Confidence Intervals	0.723 ± 0.195
Sensitivity	0.684
Positive Predictive Value	0.749
Nr of predictions	8

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...	0.94	0.94	0.94	17	339	2	0	1	1	1
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.71	0.69	0.74	20	1506	7	2	5	0	9
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.25	0.17	5	4486	37	9	16	12	15
4A1C_3	5S_rRNA links to Rfam database...	0.86	0.84	0.89	31	2728	6	0	4	2	6
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

Total Scores
MCC	0.694
Average MCC ± 95% Confidence Intervals	0.658 ± 0.199
Sensitivity	0.631
Positive Predictive Value	0.771
Nr of predictions	8

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...	0.51	0.50	0.56	9	341	8	0	7	1	9
3RKF_A	Purine links to Rfam database...	0.81	0.71	0.94	17	848	1	0	1	0	7
3SD1_A	THF links to Rfam database...	0.84	0.86	0.83	25	1503	5	4	1	0	4
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.19	5	4490	23	5	16	2	15
4A1C_3	5S_rRNA links to Rfam database...	0.90	0.84	0.97	31	2731	1	0	1	0	6
4AOB_A	SAM links to Rfam database...	0.85	0.72	1.00	21	1416	2	0	0	2	8
4ENB_A	crcB links to Rfam database...	0.51	0.27	1.00	4	468	0	0	0	0	11
4ENC_A	crcB links to Rfam database...	0.63	0.40	1.00	6	490	0	0	0	0	9

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