CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASampler(seed)		RNAwolf
MCC	0.417	>	0.340
Average MCC ± 95% Confidence Intervals	0.405 ± 0.189	>	0.378 ± 0.224
Sensitivity	0.283	<	0.333
Positive Predictive Value	0.619	>	0.353
Total TP	91	<	107
Total TN	60849	>	60693
Total FP	82	<	227
Total FP CONTRA	4	<	34
Total FP INCONS	52	<	162
Total FP COMP	26	<	31
Total FN	230	>	214
P-value	0.0

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

Total Scores
MCC	0.417
Average MCC ± 95% Confidence Intervals	0.405 ± 0.189
Sensitivity	0.283
Positive Predictive Value	0.619
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...	-0.01	0.00	0.00	0	1530	10	0	10	0	20
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
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

Total Scores
MCC	0.340
Average MCC ± 95% Confidence Intervals	0.378 ± 0.224
Sensitivity	0.333
Positive Predictive Value	0.353
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
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7470	42	4	29	9	33
3J3F_8	5_8S_rRNA links to Rfam database...	0.23	0.25	0.21	9	12204	45	5	28	12	27
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
3W3S_B	tRNA-Sec links to Rfam database...	0.68	0.63	0.74	25	4719	10	0	9	1	15
3ZEX_C	5_8S_rRNA links to Rfam database...	0.05	0.06	0.06	3	14144	49	12	37	0	49
4A1C_2	5_8S_rRNA links to Rfam database...	0.08	0.09	0.08	3	11741	46	10	27	9	30
4JF2_A	preQ1-II links to Rfam database...	0.67	0.58	0.78	18	2827	5	3	2	0	13

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