CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PETfold_pre2.0(20)		MXScarna(seed)
MCC	0.595	>	0.539
Average MCC ± 95% Confidence Intervals	0.593 ± 0.212	>	0.518 ± 0.146
Sensitivity	0.567	>	0.476
Positive Predictive Value	0.631	>	0.618
Total TP	106	>	89
Total TN	22051	<	22075
Total FP	91	<	101
Total FP CONTRA	11	<	21
Total FP INCONS	51	>	34
Total FP COMP	29	<	46
Total FN	81	<	98
P-value	0.0

Comparison of performance of PETfold_pre2.0(20) and MXScarna(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 PETfold_pre2.0(20) and MXScarna(seed)).
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 PETfold_pre2.0(20) and MXScarna(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for PETfold_pre2.0(20) and MXScarna(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 PETfold_pre2.0(20) and MXScarna(seed)).

Total Scores
MCC	0.595
Average MCC ± 95% Confidence Intervals	0.593 ± 0.212
Sensitivity	0.567
Positive Predictive Value	0.631
Nr of predictions	9

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
3J3E_8	5_8S_rRNA links to Rfam database...	0.48	0.47	0.50	7	2728	11	2	5	4	8
3J3F_8	5_8S_rRNA links to Rfam database...	0.34	0.37	0.32	7	4739	24	5	10	9	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.26	0.24	0.29	7	5350	20	1	16	3	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.25	0.25	0.25	5	4496	25	2	13	10	15
4AOB_A	SAM links to Rfam database...	0.87	0.83	0.92	24	1411	4	0	2	2	5
4ENB_A	crcB links to Rfam database...	0.68	0.53	0.89	8	463	1	0	1	0	7
4ENC_A	crcB links to Rfam database...	0.61	0.53	0.73	8	485	3	0	3	0	7
4FRG_B	AdoCbl-variant links to Rfam database...	0.89	0.83	0.95	20	1181	2	0	1	1	4

Total Scores
MCC	0.539
Average MCC ± 95% Confidence Intervals	0.518 ± 0.146
Sensitivity	0.476
Positive Predictive Value	0.618
Nr of predictions	9

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.90	0.86	0.95	18	1200	1	1	0	0	3
3J3E_8	5_8S_rRNA links to Rfam database...	0.23	0.20	0.27	3	2731	14	3	5	6	12
3J3F_8	5_8S_rRNA links to Rfam database...	0.48	0.47	0.50	9	4743	21	5	4	12	10
3ZEX_C	5_8S_rRNA links to Rfam database...	0.39	0.31	0.50	9	5356	21	3	6	12	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.45	0.40	0.50	8	4500	20	4	4	12	12
4AOB_A	SAM links to Rfam database...	0.71	0.69	0.74	20	1410	10	2	5	3	9
4ENB_A	crcB links to Rfam database...	0.54	0.40	0.75	6	464	2	0	2	0	9
4ENC_A	crcB links to Rfam database...	0.48	0.40	0.60	6	486	4	1	3	0	9
4FRG_B	AdoCbl-variant links to Rfam database...	0.49	0.42	0.59	10	1185	8	2	5	1	14

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