CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	RNAalifold(20)		RNAwolf
MCC	0.664	>	0.396
Average MCC ± 95% Confidence Intervals	0.655 ± 0.152	>	0.416 ± 0.188
Sensitivity	0.618	>	0.425
Positive Predictive Value	0.721	>	0.381
Total TP	160	>	110
Total TN	25364	>	25297
Total FP	80	<	224
Total FP CONTRA	22	<	57
Total FP INCONS	40	<	122
Total FP COMP	18	<	45
Total FN	99	<	149
P-value	1.74172190343e-08

Comparison of performance of RNAalifold(20) and RNAwolf. 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 RNAalifold(20) and RNAwolf).
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 RNAalifold(20) and RNAwolf).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAalifold(20) and RNAwolf. 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 RNAalifold(20) and RNAwolf).

Total Scores
MCC	0.664
Average MCC ± 95% Confidence Intervals	0.655 ± 0.152
Sensitivity	0.618
Positive Predictive Value	0.721
Nr of predictions	12

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...	0.34	0.33	0.36	5	2728	9	3	6	0	10
3J3F_8	5_8S_rRNA links to Rfam database...	0.54	0.58	0.50	11	4739	20	4	7	9	8
3RKF_A	Purine links to Rfam database...	0.81	0.71	0.94	17	848	1	0	1	0	7
3SD1_A	THF links to Rfam database...	0.84	0.86	0.83	25	1503	5	4	1	0	4
3ZEX_C	5_8S_rRNA links to Rfam database...	0.46	0.41	0.52	12	5351	16	2	9	5	17
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.19	5	4490	23	5	16	2	15
4AOB_A	SAM links to Rfam database...	0.85	0.72	1.00	21	1416	2	0	0	2	8
4ENB_A	crcB links to Rfam database...	0.51	0.27	1.00	4	468	0	0	0	0	11
4ENC_A	crcB links to Rfam database...	0.63	0.40	1.00	6	490	0	0	0	0	9
4FRG_B	AdoCbl-variant links to Rfam database...	0.84	0.71	1.00	17	1185	0	0	0	0	7

Total Scores
MCC	0.396
Average MCC ± 95% Confidence Intervals	0.416 ± 0.188
Sensitivity	0.425
Positive Predictive Value	0.381
Nr of predictions	12

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.54	0.57	0.52	12	1196	12	2	9	1	9
3J3D_C	tRNA links to Rfam database...	0.92	0.95	0.90	18	948	3	2	0	1	1
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2719	37	6	17	14	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.28	0.37	0.23	7	4730	39	9	15	15	12
3RKF_A	Purine links to Rfam database...	0.89	0.83	0.95	20	845	1	0	1	0	4
3SD1_A	THF links to Rfam database...	0.58	0.59	0.59	17	1504	12	2	10	0	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.08	0.10	0.07	3	5328	43	18	25	0	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.12	0.15	0.10	3	4487	38	12	14	12	17
4AOB_A	SAM links to Rfam database...	0.26	0.24	0.30	7	1414	17	2	14	1	22
4ENB_A	crcB links to Rfam database...	0.45	0.40	0.55	6	461	5	1	4	0	9
4ENC_A	crcB links to Rfam database...	0.34	0.33	0.38	5	483	9	0	8	1	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.54	0.50	0.60	12	1182	8	3	5	0	12

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