CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Afold		CRWrnafold
MCC	0.728	>	0.652
Average MCC ± 95% Confidence Intervals	0.751 ± 0.171	>	0.694 ± 0.188
Sensitivity	0.756	>	0.669
Positive Predictive Value	0.710	>	0.648
Total TP	208	>	184
Total TN	14678	<	14687
Total FP	126	<	133
Total FP CONTRA	23	<	28
Total FP INCONS	62	<	72
Total FP COMP	41	>	33
Total FN	67	<	91
P-value	2.66715895098e-08

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

Total Scores
MCC	0.728
Average MCC ± 95% Confidence Intervals	0.751 ± 0.171
Sensitivity	0.756
Positive Predictive Value	0.710
Nr of predictions	19

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
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
2LDT_A	-	1.00	1.00	1.00	11	151	0	0	0	0	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
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
2YIE_X	-	0.53	0.57	0.50	4	536	8	1	3	4	3
2YIE_Z	-	-0.02	0.00	0.00	0	587	16	6	9	1	8
3J0L_1	-	0.83	0.77	0.91	10	473	5	0	1	4	3
3J0L_7	-	-0.02	0.00	0.00	0	504	15	1	14	0	10
3J0L_h	-	0.87	0.81	0.93	26	2112	5	1	1	3	6
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
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	0.652
Average MCC ± 95% Confidence Intervals	0.694 ± 0.188
Sensitivity	0.669
Positive Predictive Value	0.648
Nr of predictions	19

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LBS_A	-	1.00	1.00	1.00	14	193	0	0	0	0	0
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	513	15	3	12	0	18
2LDL_A	-	0.94	0.89	1.00	8	132	1	0	0	1	1
2LDT_A	-	1.00	1.00	1.00	11	151	0	0	0	0	0
2LHP_A	-	0.96	0.93	1.00	14	247	0	0	0	0	1
2LI4_A	-	1.00	1.00	1.00	14	175	0	0	0	0	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
2LKR_A	-	0.58	0.55	0.62	16	2414	13	4	6	3	13
2LQZ_A	-	1.00	1.00	1.00	8	124	2	0	0	2	0
2YIE_X	-	0.53	0.57	0.50	4	536	9	1	3	5	3
2YIE_Z	-	-0.02	0.00	0.00	0	587	15	6	9	0	8
3J0L_1	-	0.83	0.77	0.91	10	473	5	0	1	4	3
3J0L_7	-	-0.02	0.00	0.00	0	506	13	3	10	0	10
3J0L_h	-	0.93	0.88	1.00	28	2112	0	0	0	0	4
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
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	44	8	20	16	15
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	2	0	0	2	4

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