CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	IPknot		Alterna
MCC	0.577	>	0.500
Average MCC ± 95% Confidence Intervals	0.460 ± 0.248	>	0.431 ± 0.178
Sensitivity	0.449	>	0.432
Positive Predictive Value	0.750	>	0.590
Total TP	102	>	98
Total TN	19697	>	19667
Total FP	36	<	70
Total FP CONTRA	3	<	10
Total FP INCONS	31	<	58
Total FP COMP	2	=	2
Total FN	125	<	129
P-value	0.0

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

Total Scores
MCC	0.577
Average MCC ± 95% Confidence Intervals	0.460 ± 0.248
Sensitivity	0.449
Positive Predictive Value	0.750
Nr of predictions	9

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...	0.40	0.30	0.55	6	1529	5	1	4	0	14
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_7	-	-0.01	0.00	0.00	0	1218	7	0	7	0	17
3J0L_a	-	0.21	0.19	0.25	3	1116	9	1	8	0	13
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
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...	0.61	0.48	0.80	20	3891	5	0	5	0	22
3UZL_B	tRNA links to Rfam database...	0.72	0.54	0.95	20	3549	1	0	1	0	17

Total Scores
MCC	0.500
Average MCC ± 95% Confidence Intervals	0.431 ± 0.178
Sensitivity	0.432
Positive Predictive Value	0.590
Nr of predictions	9

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
3AMU_B	tRNA links to Rfam database...	0.64	0.59	0.70	16	2980	9	0	7	2	11
3J0L_g	-	-0.01	0.00	0.00	0	456	9	4	5	0	4
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
3J16_L	tRNA links to Rfam database...	0.63	0.53	0.76	16	2754	5	1	4	0	14
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.