CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidHomfold‑LAST		Alterna
MCC	0.596	>	0.496
Average MCC ± 95% Confidence Intervals	0.469 ± 0.244	>	0.434 ± 0.156
Sensitivity	0.427	>	0.419
Positive Predictive Value	0.840	>	0.599
Total TP	105	>	103
Total TN	20338	>	20291
Total FP	22	<	71
Total FP CONTRA	0	<	10
Total FP INCONS	20	<	59
Total FP COMP	2	=	2
Total FN	141	<	143
P-value	7.68522644707e-09

Comparison of performance of CentroidHomfold-LAST 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 CentroidHomfold‑LAST 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 CentroidHomfold‑LAST and Alterna).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidHomfold-LAST 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 CentroidHomfold‑LAST and Alterna).

Total Scores
MCC	0.596
Average MCC ± 95% Confidence Intervals	0.469 ± 0.244
Sensitivity	0.427
Positive Predictive Value	0.840
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LA5_A	-	0.46	0.26	0.83	5	624	1	0	1	0	14
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1529	11	0	11	0	20
3AMU_B	tRNA links to Rfam database...	0.82	0.70	0.95	19	2983	3	0	1	2	8
3J0L_a	-	-0.01	0.00	0.00	0	1125	3	0	3	0	16
3J0L_g	-	0.00	0.00	0.00	0	465	0	0	0	0	4
3J0L_7	-	0.60	0.41	0.88	7	1217	1	0	1	0	10
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...	0.72	0.53	1.00	18	2193	0	0	0	0	16
3SD1_A	THF links to Rfam database...	0.64	0.45	0.90	19	3895	2	0	2	0	23
3UZL_B	tRNA links to Rfam database...	0.72	0.54	0.95	20	3549	1	0	1	0	17

Total Scores
MCC	0.496
Average MCC ± 95% Confidence Intervals	0.434 ± 0.156
Sensitivity	0.419
Positive Predictive Value	0.599
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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
3AMU_B	tRNA links to Rfam database...	0.64	0.59	0.70	16	2980	9	0	7	2	11
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
3J0L_7	-	0.26	0.24	0.31	4	1212	9	0	9	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.