CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		RNAfold
MCC	0.780	>	0.705
Average MCC ± 95% Confidence Intervals	0.743 ± 0.170	>	0.708 ± 0.208
Sensitivity	0.714	>	0.704
Positive Predictive Value	0.860	>	0.714
Total TP	147	>	145
Total TN	13426	>	13394
Total FP	32	<	83
Total FP CONTRA	3	<	19
Total FP INCONS	21	<	39
Total FP COMP	8	<	25
Total FN	59	<	61
P-value	0.0

Comparison of performance of PPfold(20) and RNAfold. 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 PPfold(20) and RNAfold).
Comparison of average Matthews Correlation Coefficients (MCCs) for PPfold(20) and RNAfold. 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 PPfold(20) and RNAfold).

Total Scores
MCC	0.780
Average MCC ± 95% Confidence Intervals	0.743 ± 0.170
Sensitivity	0.714
Positive Predictive Value	0.860
Nr of predictions	9

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.66	0.50	0.90	9	347	1	0	1	0	9
3AMU_B	tRNA links to Rfam database...	1.00	1.00	1.00	19	1138	2	0	0	2	0
3RKF_A	Purine links to Rfam database...	0.86	0.79	0.95	19	846	1	0	1	0	5
3SD1_A	THF links to Rfam database...	0.81	0.76	0.88	22	1508	3	2	1	0	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.27	0.25	0.29	5	4499	16	1	11	4	15
4A1C_3	5S_rRNA links to Rfam database...	0.93	0.92	0.94	34	2727	2	0	2	0	3
4AOB_A	SAM links to Rfam database...	0.87	0.83	0.92	24	1411	4	0	2	2	5
4ENB_A	crcB links to Rfam database...	0.63	0.47	0.88	7	464	1	0	1	0	8
4ENC_A	crcB links to Rfam database...	0.64	0.53	0.80	8	486	2	0	2	0	7

Total Scores
MCC	0.705
Average MCC ± 95% Confidence Intervals	0.708 ± 0.208
Sensitivity	0.704
Positive Predictive Value	0.714
Nr of predictions	9

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
3AMU_B	tRNA links to Rfam database...	0.81	0.79	0.83	15	1139	6	0	3	3	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...	0.77	0.76	0.79	22	1505	6	4	2	0	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4482	43	11	18	14	15
4A1C_3	5S_rRNA links to Rfam database...	0.88	0.86	0.89	32	2727	7	0	4	3	5
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

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