CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	TurboFold(seed)		UNAFold
MCC	0.610	>	0.529
Average MCC ± 95% Confidence Intervals	0.598 ± 0.185	>	0.521 ± 0.201
Sensitivity	0.598	>	0.551
Positive Predictive Value	0.630	>	0.519
Total TP	177	>	163
Total TN	27052	>	27019
Total FP	148	<	215
Total FP CONTRA	36	<	48
Total FP INCONS	68	<	103
Total FP COMP	44	<	64
Total FN	119	<	133
P-value	2.66715895098e-08

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

Total Scores
MCC	0.610
Average MCC ± 95% Confidence Intervals	0.598 ± 0.185
Sensitivity	0.598
Positive Predictive Value	0.630
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...	-0.03	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
3W1K_J	tRNA-Sec links to Rfam database...	0.97	0.97	0.97	30	1647	1	1	0	0	1
3ZEX_C	5_8S_rRNA links to Rfam database...	0.49	0.45	0.54	13	5350	15	2	9	4	16
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	0.529
Average MCC ± 95% Confidence Intervals	0.521 ± 0.201
Sensitivity	0.551
Positive Predictive Value	0.519
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...	-0.03	0.00	0.00	0	513	15	3	12	0	18
3J3E_8	5_8S_rRNA links to Rfam database...	0.15	0.20	0.13	3	2718	32	6	15	11	12
3J3F_8	5_8S_rRNA links to Rfam database...	0.32	0.42	0.25	8	4729	44	12	12	20	11
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...	0.77	0.76	0.79	22	1505	6	4	2	0	7
3W1K_J	tRNA-Sec links to Rfam database...	0.97	0.97	0.97	30	1647	1	1	0	0	1
3ZEX_C	5_8S_rRNA links to Rfam database...	0.30	0.34	0.26	10	5336	43	5	23	15	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	42	11	17	14	15
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	2	0	0	2	4
4ENC_A	crcB links to Rfam database...	0.37	0.33	0.45	5	485	7	0	6	1	10
4FRN_A	AdoCbl-variant links to Rfam database...	0.48	0.46	0.52	13	1823	12	2	10	0	15
4JF2_A	preQ1-II links to Rfam database...	0.89	0.79	1.00	19	1063	0	0	0	0	5

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