CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidAlifold(seed)		RNASampler(seed)
MCC	0.620	>	0.467
Average MCC ± 95% Confidence Intervals	0.568 ± 0.144	>	0.459 ± 0.143
Sensitivity	0.407	>	0.328
Positive Predictive Value	0.949	>	0.670
Total TP	186	>	150
Total TN	91450	>	91422
Total FP	15	<	107
Total FP CONTRA	2	<	8
Total FP INCONS	8	<	66
Total FP COMP	5	<	33
Total FN	271	<	307
P-value	1.31583660336e-08

Comparison of performance of CentroidAlifold(seed) and RNASampler(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 CentroidAlifold(seed) and RNASampler(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 CentroidAlifold(seed) and RNASampler(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidAlifold(seed) and RNASampler(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 CentroidAlifold(seed) and RNASampler(seed)).

Total Scores
MCC	0.620
Average MCC ± 95% Confidence Intervals	0.568 ± 0.144
Sensitivity	0.407
Positive Predictive Value	0.949
Nr of predictions	13

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...	0.00	0.00	0.00	0	1540	0	0	0	0	20
3A3A_A	tRNA-Sec links to Rfam database...	0.85	0.73	1.00	27	3628	0	0	0	0	10
3IVN_B	Purine links to Rfam database...	0.78	0.65	0.95	20	2325	1	1	0	0	11
3J3E_8	5_8S_rRNA links to Rfam database...	0.26	0.09	0.75	3	7499	1	0	1	0	30
3J3F_8	5_8S_rRNA links to Rfam database...	0.55	0.33	0.92	12	12233	1	0	1	0	24
3JYX_4	5_8S_rRNA links to Rfam database...	0.52	0.30	0.91	10	12235	3	0	1	2	23
3O58_3	5_8S_rRNA links to Rfam database...	0.56	0.34	0.92	12	12390	1	0	1	0	23
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
3W3S_B	tRNA-Sec links to Rfam database...	0.74	0.60	0.92	24	4727	3	0	2	1	16
3ZEX_C	5_8S_rRNA links to Rfam database...	0.46	0.23	0.92	12	14183	1	1	0	0	40
4A1C_2	5_8S_rRNA links to Rfam database...	0.46	0.24	0.89	8	11772	3	0	1	2	25
4JF2_A	preQ1-II links to Rfam database...	0.72	0.52	1.00	16	2834	0	0	0	0	15

Total Scores
MCC	0.467
Average MCC ± 95% Confidence Intervals	0.459 ± 0.143
Sensitivity	0.328
Positive Predictive Value	0.670
Nr of predictions	13

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...	-0.01	0.00	0.00	0	1530	10	0	10	0	20
3A3A_A	tRNA-Sec links to Rfam database...	0.70	0.49	1.00	18	3637	0	0	0	0	19
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3J3E_8	5_8S_rRNA links to Rfam database...	0.12	0.09	0.17	3	7485	22	2	13	7	30
3J3F_8	5_8S_rRNA links to Rfam database...	0.44	0.33	0.57	12	12225	15	1	8	6	24
3JYX_4	5_8S_rRNA links to Rfam database...	0.39	0.30	0.50	10	12226	13	2	8	3	23
3O58_3	5_8S_rRNA links to Rfam database...	0.45	0.34	0.60	12	12383	12	2	6	4	23
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...	0.60	0.38	0.94	16	3899	1	0	1	0	26
3W3S_B	tRNA-Sec links to Rfam database...	0.55	0.30	1.00	12	4741	1	0	0	1	28
3ZEX_C	5_8S_rRNA links to Rfam database...	0.32	0.19	0.53	10	14177	13	1	8	4	42
4A1C_2	5_8S_rRNA links to Rfam database...	0.31	0.24	0.40	8	11761	20	0	12	8	25
4JF2_A	preQ1-II links to Rfam database...	0.57	0.32	1.00	10	2840	0	0	0	0	21

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