CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Afold		RNASLOpt
MCC	0.764	>	0.727
Average MCC ± 95% Confidence Intervals	0.812 ± 0.151	>	0.792 ± 0.148
Sensitivity	0.781	>	0.721
Positive Predictive Value	0.755	>	0.743
Total TP	207	>	191
Total TN	13770	<	13787
Total FP	108	>	90
Total FP CONTRA	16	<	20
Total FP INCONS	51	>	46
Total FP COMP	41	>	24
Total FN	58	<	74
P-value	2.69132796717e-08

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

Total Scores
MCC	0.764
Average MCC ± 95% Confidence Intervals	0.812 ± 0.151
Sensitivity	0.781
Positive Predictive Value	0.755
Nr of predictions	18

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
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LHP_A	-	1.00	1.00	1.00	15	246	0	0	0	0	0
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LJJ_A	-	1.00	1.00	1.00	7	123	3	0	0	3	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	1.00	1.00	1.00	29	2411	8	0	0	8	0
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LWK_A	-	0.85	0.82	0.90	9	197	2	0	1	1	2
3J0L_1	-	0.83	0.77	0.91	10	473	5	0	1	4	3
3J0L_h	-	0.87	0.81	0.93	26	2112	5	1	1	3	6
3J0L_7	-	-0.02	0.00	0.00	0	504	15	1	14	0	10
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3VJR_D	-	1.00	1.00	1.00	12	239	1	0	0	1	0
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	43	11	17	15	15
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	3	0	1	2	4

Total Scores
MCC	0.727
Average MCC ± 95% Confidence Intervals	0.792 ± 0.148
Sensitivity	0.721
Positive Predictive Value	0.743
Nr of predictions	18

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
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LHP_A	-	1.00	1.00	1.00	15	246	0	0	0	0	0
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LJJ_A	-	1.00	1.00	1.00	7	123	3	0	0	3	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	0.70	0.69	0.71	20	2412	13	1	7	5	9
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2LWK_A	-	0.95	0.91	1.00	10	197	1	0	0	1	1
3J0L_1	-	0.73	0.62	0.89	8	475	4	0	1	3	5
3J0L_h	-	0.81	0.66	1.00	21	2119	0	0	0	0	11
3J0L_7	-	-0.02	0.00	0.00	0	506	13	3	10	0	10
3SN2_B	IRE_II links to Rfam database...	0.95	0.92	1.00	11	143	0	0	0	0	1
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3VJR_D	-	1.00	1.00	1.00	12	239	0	0	0	0	0
4A1C_2	5_8S_rRNA links to Rfam database...	0.30	0.40	0.24	8	4482	35	13	13	9	12
4A4U_A	-	1.00	1.00	1.00	9	96	0	0	0	0	0
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4

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