CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		CentroidHomfold‑LAST
MCC	0.617	>	0.546
Average MCC ± 95% Confidence Intervals	0.608 ± 0.160	>	0.505 ± 0.185
Sensitivity	0.596	>	0.544
Positive Predictive Value	0.648	>	0.560
Total TP	204	>	186
Total TN	25798	>	25781
Total FP	151	<	181
Total FP CONTRA	44	<	51
Total FP INCONS	67	<	95
Total FP COMP	40	>	35
Total FN	138	<	156
P-value	3.05041766982e-08

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

Total Scores
MCC	0.617
Average MCC ± 95% Confidence Intervals	0.608 ± 0.160
Sensitivity	0.596
Positive Predictive Value	0.648
Nr of predictions	17

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...	0.58	0.56	0.63	10	512	6	0	6	0	8
2M58_A	-	-0.02	0.00	0.00	0	530	14	3	11	0	12
3J0L_a	-	0.80	0.73	0.89	8	402	2	0	1	1	3
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...	0.79	0.79	0.79	15	949	4	3	1	0	4
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2722	29	12	8	9	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.36	0.42	0.31	8	4735	32	9	9	14	11
3U4M_B	-	0.98	0.95	1.00	21	1255	0	0	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.87	0.85	0.90	28	1958	4	0	3	1	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.26	0.25	0.28	5	4498	26	3	10	13	15
4AOB_A	SAM links to Rfam database...	0.62	0.59	0.68	17	1412	9	2	6	1	12
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...	0.73	0.60	0.90	9	486	1	1	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.77	0.71	0.85	17	1182	3	2	1	0	7
4FRN_A	AdoCbl-variant links to Rfam database...	0.42	0.39	0.46	11	1824	13	6	7	0	17
4JF2_A	preQ1-II links to Rfam database...	0.57	0.50	0.67	12	1064	6	2	4	0	12
4JRC_A	-	0.91	0.82	1.00	14	608	0	0	0	0	3

Total Scores
MCC	0.546
Average MCC ± 95% Confidence Intervals	0.505 ± 0.185
Sensitivity	0.544
Positive Predictive Value	0.560
Nr of predictions	17

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...	-0.03	0.00	0.00	0	517	11	0	11	0	18
2M58_A	-	-0.01	0.00	0.00	0	539	5	0	5	0	12
3J0L_a	-	-0.01	0.00	0.00	0	408	3	1	2	0	11
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
3U4M_B	-	0.78	0.73	0.84	16	1257	4	0	3	1	6
3W3S_B	tRNA-Sec links to Rfam database...	0.94	0.88	1.00	29	1960	1	0	0	1	4
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
4FRN_A	AdoCbl-variant links to Rfam database...	0.37	0.46	0.32	13	1807	28	11	17	0	15
4JF2_A	preQ1-II links to Rfam database...	0.89	0.79	1.00	19	1063	0	0	0	0	5
4JRC_A	-	0.87	0.76	1.00	13	609	0	0	0	0	4

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