CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	MXScarna(seed)		TurboFold(seed)
MCC	0.539	>	0.529
Average MCC ± 95% Confidence Intervals	0.489 ± 0.137	<	0.527 ± 0.155
Sensitivity	0.413	<	0.434
Positive Predictive Value	0.709	>	0.650
Total TP	202	<	212
Total TN	79407	>	79366
Total FP	125	<	150
Total FP CONTRA	11	<	16
Total FP INCONS	72	<	98
Total FP COMP	42	>	36
Total FN	287	>	277
P-value	1.10997767043e-07

Comparison of performance of MXScarna(seed) and TurboFold(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 MXScarna(seed) and TurboFold(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 MXScarna(seed) and TurboFold(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for MXScarna(seed) and TurboFold(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 MXScarna(seed) and TurboFold(seed)).

Total Scores
MCC	0.539
Average MCC ± 95% Confidence Intervals	0.489 ± 0.137
Sensitivity	0.413
Positive Predictive Value	0.709
Nr of predictions	14

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	12	0	10	2	20
3J3E_8	5_8S_rRNA links to Rfam database...	0.16	0.09	0.27	3	7492	14	1	7	6	30
3J3F_8	5_8S_rRNA links to Rfam database...	0.45	0.33	0.60	12	12226	18	1	7	10	24
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...	0.63	0.55	0.74	23	3885	8	1	7	0	19
3W1K_J	tRNA-Sec links to Rfam database...	0.84	0.76	0.94	29	4155	2	1	1	0	9
3ZEX_C	5_8S_rRNA links to Rfam database...	0.32	0.19	0.53	10	14177	20	2	7	11	42
4A1C_3	5S_rRNA links to Rfam database...	0.75	0.65	0.88	35	7100	5	1	4	0	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.35	0.24	0.50	8	11765	20	1	7	12	25
4AOB_A	SAM links to Rfam database...	0.66	0.55	0.79	23	4342	7	0	6	1	19
4ENB_A	crcB links to Rfam database...	0.48	0.32	0.75	6	1267	2	0	2	0	13
4ENC_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1316	4	1	3	0	13
4FRN_A	AdoCbl-variant links to Rfam database...	0.62	0.53	0.73	19	5125	7	2	5	0	17
4JF2_A	preQ1-II links to Rfam database...	0.44	0.32	0.63	10	2834	6	0	6	0	21

Total Scores
MCC	0.529
Average MCC ± 95% Confidence Intervals	0.527 ± 0.155
Sensitivity	0.434
Positive Predictive Value	0.650
Nr of predictions	14

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	1525	15	2	13	0	20
3J3E_8	5_8S_rRNA links to Rfam database...	0.17	0.15	0.21	5	7479	28	2	17	9	28
3J3F_8	5_8S_rRNA links to Rfam database...	0.39	0.36	0.42	13	12215	32	2	16	14	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...	0.59	0.48	0.74	20	3889	7	1	6	0	22
3W1K_J	tRNA-Sec links to Rfam database...	0.87	0.79	0.97	30	4155	1	1	0	0	8
3ZEX_C	5_8S_rRNA links to Rfam database...	0.39	0.27	0.56	14	14171	14	2	9	3	38
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	0	6	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.15	0.15	0.15	5	11748	37	3	25	9	28
4AOB_A	SAM links to Rfam database...	0.56	0.40	0.77	17	4349	6	1	4	1	25
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10
4FRN_A	AdoCbl-variant links to Rfam database...	0.69	0.56	0.87	20	5128	3	1	2	0	16
4JF2_A	preQ1-II links to Rfam database...	0.78	0.61	1.00	19	2831	0	0	0	0	12

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