CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	TurboFold(seed)		RNASLOpt
MCC	0.504	>	0.430
Average MCC ± 95% Confidence Intervals	0.501 ± 0.179	>	0.456 ± 0.176
Sensitivity	0.416	>	0.356
Positive Predictive Value	0.616	>	0.525
Total TP	172	>	147
Total TN	73286	>	73285
Total FP	143	<	175
Total FP CONTRA	15	<	20
Total FP INCONS	92	<	113
Total FP COMP	36	<	42
Total FN	241	<	266
P-value	1.38194587311e-08

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

Total Scores
MCC	0.504
Average MCC ± 95% Confidence Intervals	0.501 ± 0.179
Sensitivity	0.416
Positive Predictive Value	0.616
Nr of predictions	12

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
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_2	5_8S_rRNA links to Rfam database...	0.15	0.15	0.15	5	11748	37	3	25	9	28
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	0	6	0	23
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

Total Scores
MCC	0.430
Average MCC ± 95% Confidence Intervals	0.456 ± 0.176
Sensitivity	0.356
Positive Predictive Value	0.525
Nr of predictions	12

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...	0.47	0.35	0.64	7	1529	4	0	4	0	13
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7483	30	1	19	10	33
3J3F_8	5_8S_rRNA links to Rfam database...	0.34	0.33	0.35	12	12212	35	3	19	13	24
3W1K_J	tRNA-Sec links to Rfam database...	0.84	0.74	0.97	28	4157	1	1	0	0	10
3ZEX_C	5_8S_rRNA links to Rfam database...	0.26	0.21	0.33	11	14163	35	2	20	13	41
4A1C_2	5_8S_rRNA links to Rfam database...	0.23	0.24	0.22	8	11744	35	8	21	6	25
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.52	0.88	28	7108	4	0	4	0	26
4AOB_A	SAM links to Rfam database...	0.26	0.19	0.38	8	4350	13	2	11	0	34
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
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...	0.20	0.17	0.26	6	5128	17	2	15	0	30
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.