CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	TurboFold(20)		RNASLOpt
MCC	0.596	>	0.480
Average MCC ± 95% Confidence Intervals	0.615 ± 0.179	>	0.514 ± 0.210
Sensitivity	0.597	>	0.500
Positive Predictive Value	0.603	>	0.470
Total TP	123	>	103
Total TN	22983	>	22968
Total FP	125	<	171
Total FP CONTRA	30	<	50
Total FP INCONS	51	<	66
Total FP COMP	44	<	55
Total FN	83	<	103
P-value	9.07229227445e-09

Comparison of performance of TurboFold(20) and RNASLOpt. 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(20) and RNASLOpt).
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(20) and RNASLOpt).
Comparison of average Matthews Correlation Coefficients (MCCs) for TurboFold(20) and RNASLOpt. 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(20) and RNASLOpt).

Total Scores
MCC	0.596
Average MCC ± 95% Confidence Intervals	0.615 ± 0.179
Sensitivity	0.597
Positive Predictive Value	0.603
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.74	0.76	0.73	16	1197	7	1	5	1	5
3J3D_C	tRNA links to Rfam database...	0.90	0.95	0.86	18	947	3	3	0	0	1
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	37	9	10	18	9
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...	0.22	0.25	0.21	5	4492	28	6	13	9	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
4FRG_B	AdoCbl-variant links to Rfam database...	0.93	0.88	1.00	21	1181	0	0	0	0	3

Total Scores
MCC	0.480
Average MCC ± 95% Confidence Intervals	0.514 ± 0.210
Sensitivity	0.500
Positive Predictive Value	0.470
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.74	0.76	0.73	16	1197	7	3	3	1	5
3J3D_C	tRNA links to Rfam database...	0.90	0.95	0.86	18	947	3	3	0	0	1
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2724	30	6	12	12	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.39	0.47	0.32	9	4733	38	10	9	19	10
3ZEX_C	5_8S_rRNA links to Rfam database...	0.32	0.34	0.31	10	5342	36	8	14	14	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.30	0.40	0.24	8	4482	35	13	13	9	12
4AOB_A	SAM links to Rfam database...	0.31	0.28	0.38	8	1416	13	3	10	0	21
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.60	0.58	0.64	14	1180	8	3	5	0	10

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