CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PETfold_pre2.0(20)		RSpredict(20)
MCC	0.718	>	0.558
Average MCC ± 95% Confidence Intervals	0.637 ± 0.179	>	0.451 ± 0.183
Sensitivity	0.682	>	0.511
Positive Predictive Value	0.758	>	0.611
Total TP	304	>	228
Total TN	183468	<	183496
Total FP	163	<	198
Total FP CONTRA	26	<	49
Total FP INCONS	71	<	96
Total FP COMP	66	>	53
Total FN	142	<	218
P-value	2.02510705504e-08

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

Total Scores
MCC	0.718
Average MCC ± 95% Confidence Intervals	0.637 ± 0.179
Sensitivity	0.682
Positive Predictive Value	0.758
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
3J2C_N	SSU_rRNA_bacteria links to Rfam database...	0.80	0.75	0.85	181	160469	69	12	20	37	59
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...	0.48	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	0.558
Average MCC ± 95% Confidence Intervals	0.451 ± 0.183
Sensitivity	0.511
Positive Predictive Value	0.611
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...	0.90	0.90	0.90	19	1198	3	1	1	1	2
3J2C_N	SSU_rRNA_bacteria links to Rfam database...	0.68	0.62	0.74	148	160482	81	14	38	29	92
3J3D_C	tRNA links to Rfam database...	0.82	0.84	0.80	16	948	4	3	1	0	3
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2724	19	5	13	1	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.42	0.47	0.38	9	4737	26	9	6	11	10
3ZEX_C	5_8S_rRNA links to Rfam database...	0.34	0.31	0.38	9	5350	19	3	12	4	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.25	0.30	0.21	6	4487	30	12	11	7	14
4AOB_A	SAM links to Rfam database...	0.33	0.21	0.55	6	1426	5	1	4	0	23
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...	0.51	0.40	0.67	6	487	3	0	3	0	9
4FRG_B	AdoCbl-variant links to Rfam database...	0.19	0.13	0.33	3	1193	6	1	5	0	21

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