CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PknotsRG		TurboFold(seed)
MCC	0.662	>	0.647
Average MCC ± 95% Confidence Intervals	0.707 ± 0.187	>	0.639 ± 0.205
Sensitivity	0.683	>	0.615
Positive Predictive Value	0.651	<	0.691
Total TP	179	>	161
Total TN	19915	<	19957
Total FP	129	>	92
Total FP CONTRA	29	>	20
Total FP INCONS	67	>	52
Total FP COMP	33	>	20
Total FN	83	<	101
P-value	1.39027542218e-05

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

Total Scores
MCC	0.662
Average MCC ± 95% Confidence Intervals	0.707 ± 0.187
Sensitivity	0.683
Positive Predictive Value	0.651
Nr of predictions	11

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...	1.00	1.00	1.00	18	339	1	0	0	1	0
2LC8_A	GP_knot1 links to Rfam database...	0.66	0.61	0.73	11	513	4	2	2	0	7
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...	0.73	0.72	0.75	21	1505	7	4	3	0	8
3ZEX_C	5_8S_rRNA links to Rfam database...	0.30	0.34	0.26	10	5336	44	5	23	16	19
4A1C_3	5S_rRNA links to Rfam database...	0.85	0.84	0.86	31	2727	8	0	5	3	6
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.25	0.14	5	4480	43	11	20	12	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...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0
4FRN_A	AdoCbl-variant links to Rfam database...	0.59	0.57	0.62	16	1822	10	2	8	0	12

Total Scores
MCC	0.647
Average MCC ± 95% Confidence Intervals	0.639 ± 0.205
Sensitivity	0.615
Positive Predictive Value	0.691
Nr of predictions	11

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
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
3ZEX_C	5_8S_rRNA links to Rfam database...	0.49	0.45	0.54	13	5350	15	2	9	4	16
4A1C_3	5S_rRNA links to Rfam database...	0.86	0.84	0.89	31	2728	6	0	4	2	6
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
4FRN_A	AdoCbl-variant links to Rfam database...	0.79	0.71	0.87	20	1825	3	1	2	0	8

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