CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidAlifold(20)		CentroidHomfold‑LAST
MCC	0.740	>	0.572
Average MCC ± 95% Confidence Intervals	0.681 ± 0.201	>	0.584 ± 0.193
Sensitivity	0.635	>	0.578
Positive Predictive Value	0.869	>	0.576
Total TP	146	>	133
Total TN	20044	>	19981
Total FP	30	<	131
Total FP CONTRA	11	<	40
Total FP INCONS	11	<	58
Total FP COMP	8	<	33
Total FN	84	<	97
P-value	1.19192530585e-08

Comparison of performance of CentroidAlifold(20) and CentroidHomfold-LAST. 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 CentroidAlifold(20) and CentroidHomfold‑LAST).
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 CentroidAlifold(20) and CentroidHomfold‑LAST).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidAlifold(20) and CentroidHomfold-LAST. 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 CentroidAlifold(20) and CentroidHomfold‑LAST).

Total Scores
MCC	0.740
Average MCC ± 95% Confidence Intervals	0.681 ± 0.201
Sensitivity	0.635
Positive Predictive Value	0.869
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	2	1	0	1	1
3J3D_C	tRNA links to Rfam database...	0.90	0.95	0.86	18	947	3	3	0	0	1
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2738	4	1	3	0	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.44	0.37	0.54	7	4748	8	3	3	2	12
3RKF_A	Purine links to Rfam database...	0.86	0.75	1.00	18	848	0	0	0	0	6
3SD1_A	THF links to Rfam database...	0.85	0.76	0.96	22	1510	1	0	1	0	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.25	0.45	5	4505	8	3	3	2	15
4AOB_A	SAM links to Rfam database...	0.89	0.79	1.00	23	1414	2	0	0	2	6
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...	0.68	0.47	1.00	7	489	0	0	0	0	8
4FRG_B	AdoCbl-variant links to Rfam database...	0.81	0.71	0.94	17	1184	2	0	1	1	7

Total Scores
MCC	0.572
Average MCC ± 95% Confidence Intervals	0.584 ± 0.193
Sensitivity	0.578
Positive Predictive Value	0.576
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...	0.41	0.52	0.34	11	1187	22	7	14	1	10
3J3D_C	tRNA links to Rfam database...	0.73	0.79	0.68	15	946	7	3	4	0	4
3J3E_8	5_8S_rRNA links to Rfam database...	0.07	0.07	0.09	1	2731	16	4	6	6	14
3J3F_8	5_8S_rRNA links to Rfam database...	0.36	0.47	0.27	9	4728	36	11	13	12	10
3RKF_A	Purine links to Rfam database...	0.86	0.75	1.00	18	848	0	0	0	0	6
3SD1_A	THF links to Rfam database...	0.77	0.66	0.90	19	1512	2	1	1	0	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.25	0.24	5	4495	29	8	8	13	15
4AOB_A	SAM links to Rfam database...	0.85	0.72	1.00	21	1416	1	0	0	1	8
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	0	0	0	0	4
4FRG_B	AdoCbl-variant links to Rfam database...	0.43	0.50	0.40	12	1172	18	6	12	0	12

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