CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidHomfold‑LAST		CentroidAlifold(seed)
MCC	0.634	>	0.575
Average MCC ± 95% Confidence Intervals	0.635 ± 0.173	>	0.531 ± 0.132
Sensitivity	0.501	>	0.355
Positive Predictive Value	0.808	<	0.937
Total TP	189	>	134
Total TN	43664	<	43755
Total FP	54	>	12
Total FP CONTRA	5	>	0
Total FP INCONS	40	>	9
Total FP COMP	9	>	3
Total FN	188	<	243
P-value	1.47941000302e-08

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

Total Scores
MCC	0.634
Average MCC ± 95% Confidence Intervals	0.635 ± 0.173
Sensitivity	0.501
Positive Predictive Value	0.808
Nr of predictions	12

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.92	0.90	0.95	18	971	1	0	1	0	2
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
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
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.18	5	11753	29	5	18	6	28
4A1C_3	5S_rRNA links to Rfam database...	0.68	0.56	0.83	30	7104	6	0	6	0	24
4AOB_A	SAM links to Rfam database...	0.71	0.50	1.00	21	4350	1	0	0	1	21
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1315	0	0	0	0	8

Total Scores
MCC	0.575
Average MCC ± 95% Confidence Intervals	0.531 ± 0.132
Sensitivity	0.355
Positive Predictive Value	0.937
Nr of predictions	12

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.53	0.50	0.59	10	973	7	0	7	0	10
2LC8_A	GP_knot1 links to Rfam database...	0.00	0.00	0.00	0	1540	0	0	0	0	20
3AMU_B	tRNA links to Rfam database...	0.47	0.22	1.00	6	2997	0	0	0	0	21
3J16_L	tRNA links to Rfam database...	0.45	0.20	1.00	6	2769	0	0	0	0	24
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...	0.71	0.52	0.96	22	3893	1	0	1	0	20
3UZL_B	tRNA links to Rfam database...	0.40	0.16	1.00	6	3564	0	0	0	0	31
4A1C_2	5_8S_rRNA links to Rfam database...	0.46	0.24	0.89	8	11772	3	0	1	2	25
4A1C_3	5S_rRNA links to Rfam database...	0.54	0.30	1.00	16	7124	0	0	0	0	38
4AOB_A	SAM links to Rfam database...	0.75	0.57	1.00	24	4347	1	0	0	1	18
4ENB_A	crcB links to Rfam database...	0.65	0.42	1.00	8	1267	0	0	0	0	11
4ENC_A	crcB links to Rfam database...	0.65	0.42	1.00	8	1318	0	0	0	0	11

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