CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		RNASLOpt
MCC	0.619	>	0.558
Average MCC ± 95% Confidence Intervals	0.583 ± 0.153	>	0.547 ± 0.139
Sensitivity	0.594	>	0.555
Positive Predictive Value	0.655	>	0.572
Total TP	243	>	227
Total TN	33014	>	32988
Total FP	178	<	227
Total FP CONTRA	50	<	73
Total FP INCONS	78	<	97
Total FP COMP	50	<	57
Total FN	166	<	182
P-value	5.1503931209e-08

Comparison of performance of ContextFold and RNASLOpt. 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 RNASLOpt).
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 RNASLOpt).
Comparison of average Matthews Correlation Coefficients (MCCs) for ContextFold and RNASLOpt. 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 RNASLOpt).

Total Scores
MCC	0.619
Average MCC ± 95% Confidence Intervals	0.583 ± 0.153
Sensitivity	0.594
Positive Predictive Value	0.655
Nr of predictions	20

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
3W1K_J	tRNA-Sec links to Rfam database...	0.90	0.87	0.93	27	1649	2	1	1	0	4
3W3S_B	tRNA-Sec links to Rfam database...	0.87	0.85	0.90	28	1958	4	0	3	1	5
3ZEX_C	5_8S_rRNA links to Rfam database...	0.44	0.41	0.48	12	5349	23	4	9	10	17
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
4ATO_G	-	-0.02	0.00	0.00	0	218	2	1	1	0	7
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	0.558
Average MCC ± 95% Confidence Intervals	0.547 ± 0.139
Sensitivity	0.555
Positive Predictive Value	0.572
Nr of predictions	20

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...	0.48	0.39	0.64	7	517	4	0	4	0	11
2M58_A	-	0.37	0.33	0.44	4	535	5	4	1	0	8
3J0L_a	-	0.21	0.18	0.29	2	404	6	3	2	1	9
3J20_0	tRNA links to Rfam database...	0.74	0.76	0.73	16	1197	7	3	3	1	5
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...	-0.01	0.00	0.00	0	2724	30	6	12	12	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.39	0.47	0.32	9	4733	38	10	9	19	10
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3W1K_J	tRNA-Sec links to Rfam database...	0.93	0.90	0.97	28	1649	1	1	0	0	3
3W3S_B	tRNA-Sec links to Rfam database...	0.90	0.85	0.97	28	1960	2	0	1	1	5
3ZEX_C	5_8S_rRNA links to Rfam database...	0.32	0.34	0.31	10	5342	36	8	14	14	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.30	0.40	0.24	8	4482	35	13	13	9	12
4AOB_A	SAM links to Rfam database...	0.31	0.28	0.38	8	1416	13	3	10	0	21
4ATO_G	-	0.36	0.43	0.33	3	211	6	6	0	0	4
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...	0.73	0.60	0.90	9	486	1	1	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.60	0.58	0.64	14	1180	8	3	5	0	10
4FRN_A	AdoCbl-variant links to Rfam database...	0.19	0.18	0.22	5	1825	18	6	12	0	23
4JF2_A	preQ1-II links to Rfam database...	0.89	0.79	1.00	19	1063	0	0	0	0	5
4JRC_A	-	0.97	0.94	1.00	16	606	0	0	0	0	1

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