CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidHomfold‑LAST		RSpredict(seed)
MCC	0.753	>	0.264
Average MCC ± 95% Confidence Intervals	0.743 ± 0.195	>	0.202 ± 0.183
Sensitivity	0.690	>	0.149
Positive Predictive Value	0.829	>	0.488
Total TP	180	>	39
Total TN	16360	<	16497
Total FP	63	>	43
Total FP CONTRA	9	>	8
Total FP INCONS	28	<	33
Total FP COMP	26	>	2
Total FN	81	<	222
P-value	1.13392142882e-08

Comparison of performance of CentroidHomfold-LAST and RSpredict(seed). 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 CentroidHomfold‑LAST and RSpredict(seed)).
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 CentroidHomfold‑LAST and RSpredict(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidHomfold-LAST and RSpredict(seed). 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 CentroidHomfold‑LAST and RSpredict(seed)).

Total Scores
MCC	0.753
Average MCC ± 95% Confidence Intervals	0.743 ± 0.195
Sensitivity	0.690
Positive Predictive Value	0.829
Nr of predictions	12

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...	0.94	0.94	0.94	17	339	2	0	1	1	1
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	517	11	0	11	0	18
3AMU_B	tRNA links to Rfam database...	0.95	0.95	0.95	18	1138	4	0	1	3	1
3J16_L	tRNA links to Rfam database...	0.90	0.81	1.00	17	1142	0	0	0	0	4
3RKF_A	Purine links to Rfam database...	0.86	0.75	1.00	18	848	0	0	0	0	6
3SD1_A	THF links to Rfam database...	0.77	0.66	0.90	19	1512	2	1	1	0	10
3UZL_B	tRNA links to Rfam database...	0.93	0.88	1.00	14	1279	7	0	0	7	2
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.25	0.24	5	4495	29	8	8	13	15
4A1C_3	5S_rRNA links to Rfam database...	0.80	0.78	0.83	29	2728	7	0	6	1	8
4AOB_A	SAM links to Rfam database...	0.85	0.72	1.00	21	1416	1	0	0	1	8
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...	0.85	0.73	1.00	11	485	0	0	0	0	4

Total Scores
MCC	0.264
Average MCC ± 95% Confidence Intervals	0.202 ± 0.183
Sensitivity	0.149
Positive Predictive Value	0.488
Nr of predictions	12

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...	0.55	0.50	0.64	9	343	6	0	5	1	9
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	515	13	0	13	0	18
3AMU_B	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1155	2	0	2	0	19
3J16_L	tRNA links to Rfam database...	0.00	0.00	0.00	0	1158	1	0	1	0	21
3RKF_A	Purine links to Rfam database...	0.84	0.75	0.95	18	847	1	1	0	0	6
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	1533	0	0	0	0	29
3UZL_B	tRNA links to Rfam database...	-0.01	0.00	0.00	0	1287	6	3	3	0	16
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	4512	5	2	2	1	20
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2759	4	2	2	0	37
4AOB_A	SAM links to Rfam database...	0.42	0.21	0.86	6	1430	1	0	1	0	23
4ENB_A	crcB links to Rfam database...	0.34	0.20	0.60	3	467	2	0	2	0	12
4ENC_A	crcB links to Rfam database...	0.34	0.20	0.60	3	491	2	0	2	0	12

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