CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidHomfold‑LAST		RSpredict(20)
MCC	0.725	>	0.642
Average MCC ± 95% Confidence Intervals	0.716 ± 0.123	>	0.599 ± 0.125
Sensitivity	0.726	>	0.588
Positive Predictive Value	0.731	>	0.708
Total TP	342	>	277
Total TN	37815	<	37892
Total FP	193	>	157
Total FP CONTRA	41	>	39
Total FP INCONS	85	>	75
Total FP COMP	67	>	43
Total FN	129	<	194
P-value	5.10776592382e-08

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

Total Scores
MCC	0.725
Average MCC ± 95% Confidence Intervals	0.716 ± 0.123
Sensitivity	0.726
Positive Predictive Value	0.731
Nr of predictions	20

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.94	0.94	0.94	17	339	2	0	1	1	1
3AMU_B	tRNA links to Rfam database...	0.95	0.95	0.95	18	1138	4	0	1	3	1
3J20_0	tRNA links to Rfam database...	0.41	0.52	0.34	11	1187	22	7	14	1	10
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J2L_3	5S_rRNA links to Rfam database...	0.94	0.94	0.94	32	2986	8	0	2	6	2
3J3D_C	tRNA links to Rfam database...	0.73	0.79	0.68	15	946	7	3	4	0	4
3J3E_7	5S_rRNA links to Rfam database...	0.85	0.85	0.85	29	2707	9	0	5	4	5
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
3J3F_7	5S_rRNA links to Rfam database...	0.79	0.81	0.78	29	2897	10	1	7	2	7
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
3ZEX_D	5S_rRNA links to Rfam database...	0.86	0.83	0.91	29	2764	8	0	3	5	6
3ZND_W	tRNA links to Rfam database...	0.75	0.75	0.75	6	1183	13	0	2	11	2
4A1C_3	5S_rRNA links to Rfam database...	0.80	0.78	0.83	29	2728	7	0	6	1	8
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

Total Scores
MCC	0.642
Average MCC ± 95% Confidence Intervals	0.599 ± 0.125
Sensitivity	0.588
Positive Predictive Value	0.708
Nr of predictions	20

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.53	0.50	0.60	9	342	7	0	6	1	9
3AMU_B	tRNA links to Rfam database...	0.69	0.53	0.91	10	1146	2	0	1	1	9
3J20_0	tRNA links to Rfam database...	0.90	0.90	0.90	19	1198	3	1	1	1	2
3J20_1	tRNA links to Rfam database...	0.67	0.50	0.91	10	1101	2	0	1	1	10
3J2L_3	5S_rRNA links to Rfam database...	0.71	0.59	0.87	20	2997	6	0	3	3	14
3J3D_C	tRNA links to Rfam database...	0.82	0.84	0.80	16	948	4	3	1	0	3
3J3E_7	5S_rRNA links to Rfam database...	0.82	0.79	0.84	27	2709	7	0	5	2	7
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
3J3F_7	5S_rRNA links to Rfam database...	0.94	0.94	0.94	34	2898	3	1	1	1	2
3RKF_A	Purine links to Rfam database...	0.91	0.88	0.95	21	844	1	1	0	0	3
3SD1_A	THF links to Rfam database...	0.82	0.86	0.78	25	1501	7	5	2	0	4
3ZEX_D	5S_rRNA links to Rfam database...	0.88	0.83	0.94	29	2765	7	0	2	5	6
3ZND_W	tRNA links to Rfam database...	0.47	0.38	0.60	3	1186	9	0	2	7	5
4A1C_3	5S_rRNA links to Rfam database...	0.60	0.49	0.75	18	2739	8	0	6	2	19
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.