CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		Alterna
MCC	0.782	>	0.691
Average MCC ± 95% Confidence Intervals	0.772 ± 0.206	>	0.713 ± 0.199
Sensitivity	0.757	>	0.701
Positive Predictive Value	0.820	>	0.697
Total TP	109	>	101
Total TN	5225	>	5213
Total FP	36	<	63
Total FP CONTRA	3	<	15
Total FP INCONS	21	<	29
Total FP COMP	12	<	19
Total FN	35	<	43
P-value	2.00627773251e-08

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

Total Scores
MCC	0.782
Average MCC ± 95% Confidence Intervals	0.772 ± 0.206
Sensitivity	0.757
Positive Predictive Value	0.820
Nr of predictions	14

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
2LDL_A	-	1.00	1.00	1.00	9	131	0	0	0	0	0
2LK3_A	-	0.94	0.89	1.00	8	92	0	0	0	0	1
3J0L_7	-	-0.02	0.00	0.00	0	506	13	3	10	0	10
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_g	-	-0.01	0.00	0.00	0	174	3	0	2	1	2
3J0L_a	-	0.80	0.73	0.89	8	402	2	0	1	1	3
3J0L_1	-	0.75	0.69	0.82	9	473	5	0	2	3	4
3J16_L	tRNA links to Rfam database...	0.90	0.81	1.00	17	1142	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
3TRZ_Z	-	1.00	1.00	1.00	5	87	0	0	0	0	0
3TS0_U	-	1.00	1.00	1.00	6	112	0	0	0	0	0
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0
3UZL_B	tRNA links to Rfam database...	0.93	0.88	1.00	14	1279	7	0	0	7	2

Total Scores
MCC	0.691
Average MCC ± 95% Confidence Intervals	0.713 ± 0.199
Sensitivity	0.701
Positive Predictive Value	0.697
Nr of predictions	14

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...	0.47	0.44	0.53	8	513	7	0	7	0	10
2LDL_A	-	1.00	1.00	1.00	9	131	1	0	0	1	0
2LK3_A	-	1.00	1.00	1.00	9	91	0	0	0	0	0
3J0L_7	-	0.37	0.40	0.36	4	508	9	2	5	2	6
3J0L_8	-	1.00	1.00	1.00	7	69	0	0	0	0	0
3J0L_g	-	-0.02	0.00	0.00	0	169	9	3	4	2	2
3J0L_a	-	0.18	0.18	0.22	2	402	8	3	4	1	9
3J0L_1	-	0.63	0.62	0.67	8	472	8	0	4	4	5
3J16_L	tRNA links to Rfam database...	0.76	0.76	0.76	16	1138	5	3	2	0	5
3SN2_B	IRE_II links to Rfam database...	0.91	0.83	1.00	10	144	0	0	0	0	2
3TRZ_Z	-	1.00	1.00	1.00	5	87	2	0	0	2	0
3TS0_U	-	1.00	1.00	1.00	6	112	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	103	0	0	0	0	0
3UZL_B	tRNA links to Rfam database...	0.68	0.75	0.63	12	1274	13	4	3	6	4

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