CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Afold		ContextFold
MCC	0.373	>	0.332
Average MCC ± 95% Confidence Intervals	0.434 ± 0.137	<	0.454 ± 0.294
Sensitivity	0.410	>	0.333
Positive Predictive Value	0.342	>	0.333
Total TP	207	>	168
Total TN	433655	<	433757
Total FP	475	>	377
Total FP CONTRA	107	>	81
Total FP INCONS	292	>	255
Total FP COMP	76	>	41
Total FN	298	<	337
P-value	0.00890162725214

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

Total Scores
MCC	0.373
Average MCC ± 95% Confidence Intervals	0.434 ± 0.137
Sensitivity	0.410
Positive Predictive Value	0.342
Nr of predictions	10

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	6	0	5	1	7
2M58_A	-	0.40	0.42	0.42	5	532	8	1	6	1	7
3J3E_8	5_8S_rRNA links to Rfam database...	0.26	0.33	0.21	5	2718	31	6	13	12	10
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3W3S_B	tRNA-Sec links to Rfam database...	0.55	0.55	0.56	18	1957	15	4	10	1	15
3ZEX_B	-	0.34	0.38	0.31	132	420926	337	77	217	43	214
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	43	11	17	15	15
4ATO_G	-	0.38	0.43	0.38	3	212	6	5	0	1	4
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	3	0	1	2	4
4JRC_A	-	0.27	0.29	0.29	5	605	12	0	12	0	12

Total Scores
MCC	0.332
Average MCC ± 95% Confidence Intervals	0.454 ± 0.294
Sensitivity	0.333
Positive Predictive Value	0.333
Nr of predictions	10

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
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2722	29	12	8	9	15
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
3ZEX_B	-	0.23	0.23	0.23	81	420993	296	62	216	18	265
4A1C_2	5_8S_rRNA links to Rfam database...	0.26	0.25	0.28	5	4498	26	3	10	13	15
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
4JRC_A	-	0.91	0.82	1.00	14	608	0	0	0	0	3

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