CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		RNAfold
MCC	0.596	>	0.474
Average MCC ± 95% Confidence Intervals	0.581 ± 0.145	>	0.476 ± 0.096
Sensitivity	0.588	>	0.503
Positive Predictive Value	0.604	>	0.448
Total TP	686	>	587
Total TN	875970	>	875795
Total FP	562	<	883
Total FP CONTRA	127	<	178
Total FP INCONS	322	<	545
Total FP COMP	113	<	160
Total FN	481	<	580
P-value	5.6410608252e-08

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

Total Scores
MCC	0.596
Average MCC ± 95% Confidence Intervals	0.581 ± 0.145
Sensitivity	0.588
Positive Predictive Value	0.604
Nr of predictions	22

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
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.89	0.88	0.89	362	421963	88	15	28	45	50
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_B	-	0.23	0.23	0.23	81	420993	296	62	216	18	265
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	0.474
Average MCC ± 95% Confidence Intervals	0.476 ± 0.096
Sensitivity	0.503
Positive Predictive Value	0.448
Nr of predictions	22

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...	0.64	0.61	0.69	11	512	5	0	5	0	7
2M58_A	-	0.40	0.42	0.42	5	532	7	1	6	0	7
3J0L_a	-	0.18	0.18	0.22	2	402	8	3	4	1	9
3J20_0	tRNA links to Rfam database...	0.51	0.57	0.48	12	1194	14	3	10	1	9
3J20_2	SSU_rRNA_archaea links to Rfam database...	0.56	0.58	0.54	238	421930	251	36	164	51	174
3J3D_C	tRNA links to Rfam database...	0.33	0.37	0.32	7	946	15	3	12	0	12
3J3E_8	5_8S_rRNA links to Rfam database...	0.25	0.33	0.20	5	2717	31	7	13	11	10
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.42	0.27	8	4731	42	10	12	20	11
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3W1K_J	tRNA-Sec links to Rfam database...	0.97	0.97	0.97	30	1647	1	1	0	0	1
3W3S_B	tRNA-Sec links to Rfam database...	0.60	0.61	0.61	20	1956	14	4	9	1	13
3ZEX_B	-	0.35	0.39	0.32	136	420925	333	77	214	42	210
3ZEX_C	5_8S_rRNA links to Rfam database...	0.30	0.34	0.26	10	5336	43	5	23	15	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4482	43	11	18	14	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ATO_G	-	0.38	0.43	0.38	3	212	5	5	0	0	4
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.37	0.33	0.45	5	485	7	0	6	1	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.36	0.38	0.38	9	1178	15	2	13	0	15
4FRN_A	AdoCbl-variant links to Rfam database...	0.59	0.57	0.62	16	1822	10	2	8	0	12
4JF2_A	preQ1-II links to Rfam database...	0.86	0.79	0.95	19	1062	1	1	0	0	5
4JRC_A	-	0.34	0.35	0.35	6	605	11	0	11	0	11

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