CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidAlifold(seed)		RNASLOpt
MCC	0.646	>	0.560
Average MCC ± 95% Confidence Intervals	0.577 ± 0.221	<	0.582 ± 0.174
Sensitivity	0.427	<	0.526
Positive Predictive Value	0.986	>	0.608
Total TP	73	<	90
Total TN	12590	>	12516
Total FP	7	<	72
Total FP CONTRA	1	<	18
Total FP INCONS	0	<	40
Total FP COMP	6	<	14
Total FN	98	>	81
P-value	0.0

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

Total Scores
MCC	0.646
Average MCC ± 95% Confidence Intervals	0.577 ± 0.221
Sensitivity	0.427
Positive Predictive Value	0.986
Nr of predictions	8

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
3J16_L	tRNA links to Rfam database...	0.53	0.29	1.00	6	1153	0	0	0	0	15
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	0.560
Average MCC ± 95% Confidence Intervals	0.582 ± 0.174
Sensitivity	0.526
Positive Predictive Value	0.608
Nr of predictions	8

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...	0.48	0.39	0.64	7	517	4	0	4	0	11
3J16_L	tRNA links to Rfam database...	0.63	0.57	0.71	12	1142	5	0	5	0	9
3UZL_B	tRNA links to Rfam database...	0.55	0.50	0.62	8	1280	9	1	4	4	8
4A1C_3	5S_rRNA links to Rfam database...	0.79	0.73	0.87	27	2732	5	0	4	1	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.30	0.40	0.24	8	4482	35	13	13	9	12
4AOB_A	SAM links to Rfam database...	0.31	0.28	0.38	8	1416	13	3	10	0	21
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...	0.73	0.60	0.90	9	486	1	1	0	0	6

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