CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	TurboFold(seed)		Vsfold5
MCC	0.575	>	0.438
Average MCC ± 95% Confidence Intervals	0.575 ± 0.209	>	0.461 ± 0.273
Sensitivity	0.568	>	0.462
Positive Predictive Value	0.593	>	0.429
Total TP	134	>	109
Total TN	20055	>	20027
Total FP	132	<	185
Total FP CONTRA	33	<	47
Total FP INCONS	59	<	98
Total FP COMP	40	=	40
Total FN	102	<	127
P-value	2.08252958266e-08

Comparison of performance of TurboFold(seed) and Vsfold5. 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 TurboFold(seed) and Vsfold5).
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 TurboFold(seed) and Vsfold5).
Comparison of average Matthews Correlation Coefficients (MCCs) for TurboFold(seed) and Vsfold5. 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 TurboFold(seed) and Vsfold5).

Total Scores
MCC	0.575
Average MCC ± 95% Confidence Intervals	0.575 ± 0.209
Sensitivity	0.568
Positive Predictive Value	0.593
Nr of predictions	11

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...	-0.03	0.00	0.00	0	513	15	3	12	0	18
3J3E_8	5_8S_rRNA links to Rfam database...	0.27	0.33	0.23	5	2720	28	6	11	11	10
3J3F_8	5_8S_rRNA links to Rfam database...	0.42	0.53	0.34	10	4732	35	9	10	16	9
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.71	0.69	0.74	20	1506	7	2	5	0	9
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.25	0.17	5	4486	37	9	16	12	15
4AOB_A	SAM links to Rfam database...	0.67	0.59	0.77	17	1415	6	2	3	1	12
4ENB_A	crcB links to Rfam database...	0.77	0.60	1.00	9	463	0	0	0	0	6
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6
4FRN_A	AdoCbl-variant links to Rfam database...	0.79	0.71	0.87	20	1825	3	1	2	0	8
4JF2_A	preQ1-II links to Rfam database...	0.89	0.79	1.00	19	1063	0	0	0	0	5

Total Scores
MCC	0.438
Average MCC ± 95% Confidence Intervals	0.461 ± 0.273
Sensitivity	0.462
Positive Predictive Value	0.429
Nr of predictions	11

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...	-0.03	0.00	0.00	0	515	13	0	13	0	18
3J3E_8	5_8S_rRNA links to Rfam database...	0.10	0.13	0.08	2	2718	31	10	12	9	13
3J3F_8	5_8S_rRNA links to Rfam database...	0.36	0.47	0.27	9	4728	38	13	11	14	10
3RKF_A	Purine links to Rfam database...	0.90	0.92	0.88	22	841	3	3	0	0	2
3SD1_A	THF links to Rfam database...	0.13	0.14	0.15	4	1507	22	5	17	0	25
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.40	0.28	8	4487	37	8	13	16	12
4AOB_A	SAM links to Rfam database...	0.21	0.21	0.25	6	1413	19	2	16	1	23
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0
4FRN_A	AdoCbl-variant links to Rfam database...	0.15	0.14	0.17	4	1825	19	3	16	0	24
4JF2_A	preQ1-II links to Rfam database...	0.96	1.00	0.92	24	1056	2	2	0	0	0

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