CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Cylofold		Alterna
MCC	0.629	>	0.528
Average MCC ± 95% Confidence Intervals	0.574 ± 0.134	>	0.491 ± 0.115
Sensitivity	0.531	>	0.464
Positive Predictive Value	0.753	>	0.612
Total TP	222	>	194
Total TN	36022	>	36000
Total FP	76	<	125
Total FP CONTRA	7	<	15
Total FP INCONS	66	<	108
Total FP COMP	3	>	2
Total FN	196	<	224
P-value	2.71568867205e-08

Comparison of performance of Cylofold 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 Cylofold and Alterna).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for Cylofold and Alterna).
Comparison of average Matthews Correlation Coefficients (MCCs) for Cylofold 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 Cylofold and Alterna).

Total Scores
MCC	0.629
Average MCC ± 95% Confidence Intervals	0.574 ± 0.134
Sensitivity	0.531
Positive Predictive Value	0.753
Nr of predictions	16

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2LA5_A	-	0.46	0.26	0.83	5	624	1	0	1	0	14
2LC8_A	GP_knot1 links to Rfam database...	0.61	0.55	0.69	11	1524	5	0	5	0	9
2XQD_Y	tRNA links to Rfam database...	0.81	0.78	0.84	21	2825	4	4	0	0	6
3ADB_C	-	0.78	0.71	0.87	27	4155	4	0	4	0	11
3AKZ_H	tRNA links to Rfam database...	0.66	0.57	0.76	16	2680	6	0	5	1	12
3AM1_B	-	0.76	0.63	0.92	22	3216	2	0	2	0	13
3AMU_B	tRNA links to Rfam database...	0.67	0.59	0.76	16	2982	7	0	5	2	11
3J0L_7	-	0.30	0.29	0.33	5	1210	10	0	10	0	12
3J0L_a	-	0.22	0.19	0.27	3	1117	8	1	7	0	13
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3NKB_B	-	0.40	0.31	0.53	8	2001	7	0	7	0	18
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.62	0.50	0.78	21	3889	6	0	6	0	21
3UZL_B	tRNA links to Rfam database...	0.45	0.38	0.54	14	3544	12	1	11	0	23

Total Scores
MCC	0.528
Average MCC ± 95% Confidence Intervals	0.491 ± 0.115
Sensitivity	0.464
Positive Predictive Value	0.612
Nr of predictions	16

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KX8_A	7SK links to Rfam database...	0.88	0.83	0.94	15	845	1	0	1	0	3
2LA5_A	-	0.46	0.26	0.83	5	624	1	0	1	0	14
2LC8_A	GP_knot1 links to Rfam database...	0.46	0.40	0.53	8	1525	7	0	7	0	12
2XQD_Y	tRNA links to Rfam database...	0.67	0.59	0.76	16	2829	5	0	5	0	11
3ADB_C	-	0.59	0.55	0.64	21	4153	12	0	12	0	17
3AKZ_H	tRNA links to Rfam database...	0.40	0.39	0.42	11	2675	15	4	11	0	17
3AM1_B	-	0.61	0.57	0.67	20	3210	10	1	9	0	15
3AMU_B	tRNA links to Rfam database...	0.64	0.59	0.70	16	2980	9	0	7	2	11
3J0L_7	-	0.26	0.24	0.31	4	1212	9	0	9	0	13
3J0L_a	-	0.23	0.19	0.30	3	1118	7	1	6	0	13
3J0L_g	-	-0.01	0.00	0.00	0	456	9	4	5	0	4
3J16_L	tRNA links to Rfam database...	0.63	0.53	0.76	16	2754	5	1	4	0	14
3NKB_B	-	0.35	0.31	0.42	8	1997	11	0	11	0	18
3RKF_A	Purine links to Rfam database...	0.69	0.56	0.86	19	2189	3	1	2	0	15
3SD1_A	THF links to Rfam database...	0.46	0.38	0.57	16	3888	12	1	11	0	26
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.