CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	MXScarna(20)		IPknot
MCC	0.586	>	0.571
Average MCC ± 95% Confidence Intervals	0.566 ± 0.193	<	0.581 ± 0.171
Sensitivity	0.474	>	0.463
Positive Predictive Value	0.731	>	0.710
Total TP	128	>	125
Total TN	34848	>	34847
Total FP	68	>	59
Total FP CONTRA	6	=	6
Total FP INCONS	41	<	45
Total FP COMP	21	>	8
Total FN	142	<	145
P-value	0.0

Comparison of performance of MXScarna(20) and IPknot. 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 MXScarna(20) and IPknot).
Comparison of average Matthews Correlation Coefficients (MCCs) for MXScarna(20) and IPknot. 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 MXScarna(20) and IPknot).

Total Scores
MCC	0.586
Average MCC ± 95% Confidence Intervals	0.566 ± 0.193
Sensitivity	0.474
Positive Predictive Value	0.731
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.86	0.74	1.00	20	2983	2	0	0	2	7
3RKF_A	Purine links to Rfam database...	0.72	0.53	1.00	18	2193	0	0	0	0	16
3SD1_A	THF links to Rfam database...	0.63	0.55	0.74	23	3885	8	2	6	0	19
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.15	0.21	5	11757	36	2	17	17	28
4A1C_3	5S_rRNA links to Rfam database...	0.64	0.56	0.75	30	7100	11	2	8	1	24
4AOB_A	SAM links to Rfam database...	0.62	0.55	0.72	23	4339	10	0	9	1	19
4ENB_A	crcB links to Rfam database...	0.26	0.11	0.67	2	1272	1	0	1	0	17
4ENC_A	crcB links to Rfam database...	0.60	0.37	1.00	7	1319	0	0	0	0	12

Total Scores
MCC	0.571
Average MCC ± 95% Confidence Intervals	0.581 ± 0.171
Sensitivity	0.463
Positive Predictive Value	0.710
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.61	0.48	0.80	20	3891	5	0	5	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	11755	26	4	17	5	28
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	1	5	0	23
4AOB_A	SAM links to Rfam database...	0.42	0.33	0.54	14	4345	13	1	11	1	28
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...	0.52	0.42	0.67	8	1314	4	0	4	0	11

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