CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Sfold		RNAwolf
MCC	0.595	>	0.436
Average MCC ± 95% Confidence Intervals	0.603 ± 0.167	>	0.421 ± 0.185
Sensitivity	0.574	>	0.437
Positive Predictive Value	0.629	>	0.452
Total TP	105	>	80
Total TN	11368	>	11358
Total FP	76	<	114
Total FP CONTRA	22	=	22
Total FP INCONS	40	<	75
Total FP COMP	14	<	17
Total FN	78	<	103
P-value	0.0

Comparison of performance of Sfold and RNAwolf. 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 Sfold and RNAwolf).
Comparison of average Matthews Correlation Coefficients (MCCs) for Sfold and RNAwolf. 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 Sfold and RNAwolf).

Total Scores
MCC	0.595
Average MCC ± 95% Confidence Intervals	0.603 ± 0.167
Sensitivity	0.574
Positive Predictive Value	0.629
Nr of predictions	9

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...	0.46	0.39	0.58	7	516	5	0	5	0	11
3J0L_a	-	0.55	0.64	0.50	7	397	8	5	2	1	4
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...	0.78	0.72	0.84	21	1508	4	2	2	0	8
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.25	0.19	5	4489	34	8	14	12	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	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.57	0.33	1.00	5	491	0	0	0	0	10

Total Scores
MCC	0.436
Average MCC ± 95% Confidence Intervals	0.421 ± 0.185
Sensitivity	0.437
Positive Predictive Value	0.452
Nr of predictions	9

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...	0.52	0.50	0.56	9	512	7	0	7	0	9
3J0L_a	-	0.14	0.18	0.14	2	397	13	4	8	1	9
3RKF_A	Purine links to Rfam database...	0.89	0.83	0.95	20	845	1	0	1	0	4
3SD1_A	THF links to Rfam database...	0.58	0.59	0.59	17	1504	12	2	10	0	12
3U4M_B	-	0.50	0.50	0.52	11	1255	12	1	9	2	11
4A1C_2	5_8S_rRNA links to Rfam database...	0.12	0.15	0.10	3	4487	38	12	14	12	17
4AOB_A	SAM links to Rfam database...	0.26	0.24	0.30	7	1414	17	2	14	1	22
4ENB_A	crcB links to Rfam database...	0.45	0.40	0.55	6	461	5	1	4	0	9
4ENC_A	crcB links to Rfam database...	0.34	0.33	0.38	5	483	9	0	8	1	10

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