CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	TurboFold(seed)		MaxExpect
MCC	0.560	>	0.522
Average MCC ± 95% Confidence Intervals	0.565 ± 0.318	>	0.511 ± 0.324
Sensitivity	0.533	>	0.520
Positive Predictive Value	0.602	>	0.538
Total TP	80	>	78
Total TN	9715	>	9703
Total FP	66	<	83
Total FP CONTRA	17	<	20
Total FP INCONS	36	<	47
Total FP COMP	13	<	16
Total FN	70	<	72
P-value	0.0

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

Total Scores
MCC	0.560
Average MCC ± 95% Confidence Intervals	0.565 ± 0.318
Sensitivity	0.533
Positive Predictive Value	0.602
Nr of predictions	7

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
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
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	0.522
Average MCC ± 95% Confidence Intervals	0.511 ± 0.324
Sensitivity	0.520
Positive Predictive Value	0.538
Nr of predictions	7

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
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...	0.70	0.69	0.71	20	1505	8	3	5	0	9
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	41	10	17	14	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
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...	0.36	0.33	0.42	5	484	8	0	7	1	10

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