CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		MCFold
MCC	0.641	>	0.409
Average MCC ± 95% Confidence Intervals	0.622 ± 0.182	>	0.433 ± 0.173
Sensitivity	0.587	>	0.470
Positive Predictive Value	0.707	>	0.367
Total TP	135	>	108
Total TN	23958	>	23855
Total FP	75	<	236
Total FP CONTRA	14	<	57
Total FP INCONS	42	<	129
Total FP COMP	19	<	50
Total FN	95	<	122
P-value	1.61358433984e-08

Comparison of performance of PPfold(20) 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 PPfold(20) 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 PPfold(20) and MCFold).
Comparison of average Matthews Correlation Coefficients (MCCs) for PPfold(20) 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 PPfold(20) and MCFold).

Total Scores
MCC	0.641
Average MCC ± 95% Confidence Intervals	0.622 ± 0.182
Sensitivity	0.587
Positive Predictive Value	0.707
Nr of predictions	11

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.95	0.95	0.95	20	1198	1	1	0	0	1
3J3D_C	tRNA links to Rfam database...	0.87	0.89	0.85	17	948	3	3	0	0	2
3J3E_8	5_8S_rRNA links to Rfam database...	0.21	0.20	0.23	3	2729	13	2	8	3	12
3J3F_8	5_8S_rRNA links to Rfam database...	0.37	0.37	0.37	7	4742	20	5	7	8	12
3RKF_A	Purine links to Rfam database...	0.86	0.79	0.95	19	846	1	0	1	0	5
3SD1_A	THF links to Rfam database...	0.81	0.76	0.88	22	1508	3	2	1	0	7
3ZEX_C	5_8S_rRNA links to Rfam database...	0.38	0.31	0.47	9	5355	14	0	10	4	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.27	0.25	0.29	5	4499	16	1	11	4	15
4ENB_A	crcB links to Rfam database...	0.63	0.47	0.88	7	464	1	0	1	0	8
4ENC_A	crcB links to Rfam database...	0.64	0.53	0.80	8	486	2	0	2	0	7
4FRG_B	AdoCbl-variant links to Rfam database...	0.84	0.75	0.95	18	1183	1	0	1	0	6

Total Scores
MCC	0.409
Average MCC ± 95% Confidence Intervals	0.433 ± 0.173
Sensitivity	0.470
Positive Predictive Value	0.367
Nr of predictions	11

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.66	0.71	0.63	15	1195	11	3	6	2	6
3J3D_C	tRNA links to Rfam database...	0.54	0.63	0.48	12	943	13	4	9	0	7
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_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
4FRG_B	AdoCbl-variant links to Rfam database...	0.35	0.38	0.35	9	1176	17	3	14	0	15

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