CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidAlifold(seed)		NanoFolder
MCC	0.536	>	0.290
Average MCC ± 95% Confidence Intervals	0.487 ± 0.101	>	0.315 ± 0.092
Sensitivity	0.308	>	0.301
Positive Predictive Value	0.940	>	0.288
Total TP	219	>	214
Total TN	104643	>	104134
Total FP	22	<	566
Total FP CONTRA	0	<	64
Total FP INCONS	14	<	464
Total FP COMP	8	<	38
Total FN	493	<	498
P-value	1.86109605532e-08

Comparison of performance of CentroidAlifold(seed) and NanoFolder. 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(seed) and NanoFolder).
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(seed) and NanoFolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidAlifold(seed) and NanoFolder. 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(seed) and NanoFolder).

Total Scores
MCC	0.536
Average MCC ± 95% Confidence Intervals	0.487 ± 0.101
Sensitivity	0.308
Positive Predictive Value	0.940
Nr of predictions	19

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.00	0.00	0.00	0	1540	0	0	0	0	20
3J16_L	tRNA links to Rfam database...	0.45	0.20	1.00	6	2769	0	0	0	0	24
3J20_1	tRNA links to Rfam database...	0.51	0.26	1.00	6	2920	0	0	0	0	17
3J2L_3	5S_rRNA links to Rfam database...	0.53	0.28	1.00	15	7860	2	0	0	2	38
3J3D_C	tRNA links to Rfam database...	0.46	0.21	1.00	6	2769	0	0	0	0	22
3J3E_8	5_8S_rRNA links to Rfam database...	0.26	0.09	0.75	3	7499	1	0	1	0	30
3J3E_7	5S_rRNA links to Rfam database...	0.56	0.33	0.95	18	7121	1	0	1	0	36
3J3F_8	5_8S_rRNA links to Rfam database...	0.55	0.33	0.92	12	12233	1	0	1	0	24
3J3F_7	5S_rRNA links to Rfam database...	0.58	0.34	1.00	17	7243	1	0	0	1	33
3J3V_B	5S_rRNA links to Rfam database...	0.48	0.28	0.84	16	7002	3	0	3	0	41
3UZL_B	tRNA links to Rfam database...	0.40	0.16	1.00	6	3564	0	0	0	0	31
3W3S_B	tRNA-Sec links to Rfam database...	0.74	0.60	0.92	24	4727	3	0	2	1	16
3ZEX_D	5S_rRNA links to Rfam database...	0.60	0.37	1.00	18	7003	0	0	0	0	31
3ZND_W	tRNA links to Rfam database...	0.00	0.00	0.00	0	2998	6	0	5	1	23
4A1C_3	5S_rRNA links to Rfam database...	0.54	0.30	1.00	16	7124	0	0	0	0	38
4A1C_2	5_8S_rRNA links to Rfam database...	0.46	0.24	0.89	8	11772	3	0	1	2	25
4AOB_A	SAM links to Rfam database...	0.75	0.57	1.00	24	4347	1	0	0	1	18
4ENC_A	crcB links to Rfam database...	0.65	0.42	1.00	8	1318	0	0	0	0	11
4JF2_A	preQ1-II links to Rfam database...	0.72	0.52	1.00	16	2834	0	0	0	0	15

Total Scores
MCC	0.290
Average MCC ± 95% Confidence Intervals	0.315 ± 0.092
Sensitivity	0.301
Positive Predictive Value	0.288
Nr of predictions	19

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.52	0.55	0.50	11	1518	11	0	11	0	9
3J16_L	tRNA links to Rfam database...	0.36	0.37	0.37	11	2745	19	3	16	0	19
3J20_1	tRNA links to Rfam database...	0.41	0.48	0.37	11	2896	19	5	14	0	12
3J2L_3	5S_rRNA links to Rfam database...	0.11	0.11	0.12	6	7824	46	3	42	1	47
3J3D_C	tRNA links to Rfam database...	0.70	0.71	0.69	20	2746	9	2	7	0	8
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7466	47	6	31	10	33
3J3E_7	5S_rRNA links to Rfam database...	0.35	0.33	0.37	18	7091	31	1	30	0	36
3J3F_8	5_8S_rRNA links to Rfam database...	0.27	0.33	0.22	12	12192	54	9	33	12	24
3J3F_7	5S_rRNA links to Rfam database...	0.17	0.18	0.17	9	7208	43	3	40	0	41
3J3V_B	5S_rRNA links to Rfam database...	0.24	0.23	0.27	13	6973	35	1	34	0	44
3UZL_B	tRNA links to Rfam database...	0.36	0.35	0.38	13	3536	21	3	18	0	24
3W3S_B	tRNA-Sec links to Rfam database...	0.17	0.18	0.18	7	4713	34	1	32	1	33
3ZEX_D	5S_rRNA links to Rfam database...	0.26	0.27	0.27	13	6972	36	1	35	0	36
3ZND_W	tRNA links to Rfam database...	0.18	0.22	0.17	5	2973	29	6	19	4	18
4A1C_3	5S_rRNA links to Rfam database...	0.48	0.46	0.51	25	7091	24	2	22	0	29
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11728	61	12	41	8	33
4AOB_A	SAM links to Rfam database...	0.33	0.29	0.39	12	4340	20	1	18	1	30
4ENC_A	crcB links to Rfam database...	0.57	0.58	0.58	11	1307	9	0	8	1	8
4JF2_A	preQ1-II links to Rfam database...	0.51	0.55	0.49	17	2815	18	5	13	0	14

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