CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNAwolf		Alterna
MCC	0.502	>	0.500
Average MCC ± 95% Confidence Intervals	0.431 ± 0.205	<	0.431 ± 0.178
Sensitivity	0.458	>	0.432
Positive Predictive Value	0.562	<	0.590
Total TP	104	>	98
Total TN	19648	<	19667
Total FP	85	>	70
Total FP CONTRA	8	<	10
Total FP INCONS	73	>	58
Total FP COMP	4	>	2
Total FN	123	<	129
P-value	0.0

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

Total Scores
MCC	0.502
Average MCC ± 95% Confidence Intervals	0.431 ± 0.205
Sensitivity	0.458
Positive Predictive Value	0.562
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...	0.52	0.50	0.56	10	1522	8	0	8	0	10
3AMU_B	tRNA links to Rfam database...	0.68	0.63	0.74	17	2980	9	0	6	3	10
3J0L_g	-	0.16	0.25	0.11	1	456	8	6	2	0	3
3J0L_7	-	-0.01	0.00	0.00	0	1214	11	0	11	0	17
3J0L_a	-	0.18	0.19	0.20	3	1113	12	1	11	0	13
3J16_L	tRNA links to Rfam database...	0.45	0.40	0.52	12	2752	11	0	11	0	18
3RKF_A	Purine links to Rfam database...	0.72	0.62	0.84	21	2186	4	0	4	0	13
3SD1_A	THF links to Rfam database...	0.46	0.43	0.50	18	3880	18	0	18	0	24
3UZL_B	tRNA links to Rfam database...	0.72	0.59	0.88	22	3545	4	1	2	1	15

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.