CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		Alterna
MCC	0.690	>	0.601
Average MCC ± 95% Confidence Intervals	0.714 ± 0.193	>	0.664 ± 0.192
Sensitivity	0.587	>	0.537
Positive Predictive Value	0.819	>	0.684
Total TP	118	>	108
Total TN	13746	>	13732
Total FP	27	<	56
Total FP CONTRA	1	<	8
Total FP INCONS	25	<	42
Total FP COMP	1	<	6
Total FN	83	<	93
P-value	2.32677072069e-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 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).
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	0.690
Average MCC ± 95% Confidence Intervals	0.714 ± 0.193
Sensitivity	0.587
Positive Predictive Value	0.819
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...	0.55	0.50	0.63	10	1524	6	0	6	0	10
2LDL_A	-	0.90	0.82	1.00	9	342	0	0	0	0	2
2LK3_A	-	0.89	0.80	1.00	8	268	0	0	0	0	2
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_g	-	-0.01	0.00	0.00	0	462	3	1	2	0	4
3J0L_a	-	0.71	0.56	0.90	9	1118	1	0	1	0	7
3J0L_1	-	0.70	0.58	0.85	11	1212	3	0	2	1	8
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3SN2_B	IRE_II links to Rfam database...	0.96	0.92	1.00	11	395	0	0	0	0	1
3TRZ_Z	-	0.91	0.83	1.00	5	205	0	0	0	0	1
3TS0_U	-	1.00	1.00	1.00	6	247	0	0	0	0	0
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3UZL_B	tRNA links to Rfam database...	0.72	0.54	0.95	20	3549	1	0	1	0	17

Total Scores
MCC	0.601
Average MCC ± 95% Confidence Intervals	0.664 ± 0.192
Sensitivity	0.537
Positive Predictive Value	0.684
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...	0.46	0.40	0.53	8	1525	7	0	7	0	12
2LDL_A	-	0.90	0.82	1.00	9	342	1	0	0	1	2
2LK3_A	-	0.95	0.90	1.00	9	267	0	0	0	0	1
3J0L_7	-	0.26	0.24	0.31	4	1212	9	0	9	0	13
3J0L_8	-	0.93	0.88	1.00	7	183	0	0	0	0	1
3J0L_g	-	-0.01	0.00	0.00	0	456	9	4	5	0	4
3J0L_a	-	0.23	0.19	0.30	3	1118	7	1	6	0	13
3J0L_1	-	0.61	0.53	0.71	10	1211	6	0	4	2	9
3J16_L	tRNA links to Rfam database...	0.63	0.53	0.76	16	2754	5	1	4	0	14
3SN2_B	IRE_II links to Rfam database...	0.91	0.83	1.00	10	396	0	0	0	0	2
3TRZ_Z	-	0.91	0.83	1.00	5	205	2	0	0	2	1
3TS0_U	-	1.00	1.00	1.00	6	247	1	0	0	1	0
3TS2_V	-	1.00	1.00	1.00	5	271	0	0	0	0	0
3UZL_B	tRNA links to Rfam database...	0.52	0.43	0.64	16	3545	9	2	7	0	21

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