CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidAlifold(seed)		RNAwolf
MCC	0.694	>	0.499
Average MCC ± 95% Confidence Intervals	0.626 ± 0.172	>	0.522 ± 0.175
Sensitivity	0.494	>	0.490
Positive Predictive Value	0.984	>	0.524
Total TP	120	>	119
Total TN	16098	>	15993
Total FP	9	<	134
Total FP CONTRA	1	<	20
Total FP INCONS	1	<	88
Total FP COMP	7	<	26
Total FN	123	<	124
P-value	1.47941000302e-08

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

Total Scores
MCC	0.694
Average MCC ± 95% Confidence Intervals	0.626 ± 0.172
Sensitivity	0.494
Positive Predictive Value	0.984
Nr of predictions	11

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...	0.00	0.00	0.00	0	528	0	0	0	0	18
3AMU_B	tRNA links to Rfam database...	0.51	0.26	1.00	5	1152	1	0	0	1	14
3J16_L	tRNA links to Rfam database...	0.53	0.29	1.00	6	1153	0	0	0	0	15
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...	0.85	0.76	0.96	22	1510	1	0	1	0	7
3UZL_B	tRNA links to Rfam database...	0.50	0.25	1.00	4	1289	2	0	0	2	12
4A1C_3	5S_rRNA links to Rfam database...	0.66	0.43	1.00	16	2747	0	0	0	0	21
4A1C_2	5_8S_rRNA links to Rfam database...	0.60	0.40	0.89	8	4507	3	1	0	2	12
4AOB_A	SAM links to Rfam database...	0.89	0.79	1.00	23	1414	2	0	0	2	6
4ENB_A	crcB links to Rfam database...	0.72	0.53	1.00	8	464	0	0	0	0	7
4ENC_A	crcB links to Rfam database...	0.73	0.53	1.00	8	488	0	0	0	0	7

Total Scores
MCC	0.499
Average MCC ± 95% Confidence Intervals	0.522 ± 0.175
Sensitivity	0.490
Positive Predictive Value	0.524
Nr of predictions	11

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
3AMU_B	tRNA links to Rfam database...	0.77	0.79	0.75	15	1137	8	0	5	3	4
3J16_L	tRNA links to Rfam database...	0.58	0.57	0.60	12	1139	9	2	6	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
3UZL_B	tRNA links to Rfam database...	0.93	0.88	1.00	14	1279	7	0	0	7	2
4A1C_3	5S_rRNA links to Rfam database...	0.32	0.30	0.35	11	2732	21	1	19	1	26
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.