CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	TurboFold(seed)		MCFold
MCC	0.618	>	0.470
Average MCC ± 95% Confidence Intervals	0.611 ± 0.188	>	0.488 ± 0.197
Sensitivity	0.612	>	0.519
Positive Predictive Value	0.633	>	0.438
Total TP	178	>	151
Total TN	27057	>	26993
Total FP	149	<	250
Total FP CONTRA	33	<	50
Total FP INCONS	70	<	144
Total FP COMP	46	<	56
Total FN	113	<	140
P-value	2.26346675981e-08

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

Total Scores
MCC	0.618
Average MCC ± 95% Confidence Intervals	0.611 ± 0.188
Sensitivity	0.612
Positive Predictive Value	0.633
Nr of predictions	13

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
3J3E_8	5_8S_rRNA links to Rfam database...	0.27	0.33	0.23	5	2720	28	6	11	11	10
3J3F_8	5_8S_rRNA links to Rfam database...	0.42	0.53	0.34	10	4732	35	9	10	16	9
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
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
4JF2_A	preQ1-II links to Rfam database...	0.89	0.79	1.00	19	1063	0	0	0	0	5

Total Scores
MCC	0.470
Average MCC ± 95% Confidence Intervals	0.488 ± 0.197
Sensitivity	0.519
Positive Predictive Value	0.438
Nr of predictions	13

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...	0.44	0.44	0.47	8	511	10	0	9	1	10
3J3E_8	5_8S_rRNA links to Rfam database...	0.15	0.20	0.12	3	2716	36	11	12	13	12
3J3F_8	5_8S_rRNA links to Rfam database...	0.14	0.21	0.10	4	4720	51	17	20	14	15
3RKF_A	Purine links to Rfam database...	0.89	0.88	0.91	21	843	3	0	2	1	3
3SD1_A	THF links to Rfam database...	0.43	0.45	0.43	13	1503	17	1	16	0	16
3ZEX_C	5_8S_rRNA links to Rfam database...	0.30	0.34	0.27	10	5337	28	6	21	1	19
4A1C_3	5S_rRNA links to Rfam database...	0.86	0.86	0.86	32	2726	9	0	5	4	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.25	0.14	5	4480	45	12	19	14	15
4ENB_A	crcB links to Rfam database...	0.78	0.73	0.85	11	459	4	0	2	2	4
4ENC_A	crcB links to Rfam database...	0.34	0.33	0.38	5	483	11	0	8	3	10
4FRN_A	AdoCbl-variant links to Rfam database...	0.09	0.11	0.10	3	1818	28	2	25	1	25
4JF2_A	preQ1-II links to Rfam database...	0.74	0.75	0.75	18	1058	7	1	5	1	6

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