CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASLOpt		RSpredict(seed)
MCC	0.474	>	0.110
Average MCC ± 95% Confidence Intervals	0.505 ± 0.158	>	0.117 ± 0.140
Sensitivity	0.374	>	0.047
Positive Predictive Value	0.609	>	0.267
Total TP	95	>	12
Total TN	33622	<	33733
Total FP	67	>	34
Total FP CONTRA	11	>	2
Total FP INCONS	50	>	31
Total FP COMP	6	>	1
Total FN	159	<	242
P-value	0.0

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

Total Scores
MCC	0.474
Average MCC ± 95% Confidence Intervals	0.505 ± 0.158
Sensitivity	0.374
Positive Predictive Value	0.609
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...	0.47	0.35	0.64	7	1529	4	0	4	0	13
3J16_L	tRNA links to Rfam database...	0.53	0.40	0.71	12	2758	5	0	5	0	18
3UZL_B	tRNA links to Rfam database...	0.48	0.32	0.71	12	3553	5	0	5	0	25
4A1C_3	5S_rRNA links to Rfam database...	0.67	0.52	0.88	28	7108	4	0	4	0	26
4A1C_2	5_8S_rRNA links to Rfam database...	0.23	0.24	0.22	8	11744	35	8	21	6	25
4AOB_A	SAM links to Rfam database...	0.26	0.19	0.38	8	4350	13	2	11	0	34
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...	0.65	0.47	0.90	9	1316	1	1	0	0	10

Total Scores
MCC	0.110
Average MCC ± 95% Confidence Intervals	0.117 ± 0.140
Sensitivity	0.047
Positive Predictive Value	0.267
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...	-0.01	0.00	0.00	0	1527	13	0	13	0	20
3J16_L	tRNA links to Rfam database...	0.00	0.00	0.00	0	2774	1	0	1	0	30
3UZL_B	tRNA links to Rfam database...	0.00	0.00	0.00	0	3564	6	0	6	0	37
4A1C_3	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7136	4	1	3	0	54
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11777	5	1	3	1	33
4AOB_A	SAM links to Rfam database...	0.35	0.14	0.86	6	4364	1	0	1	0	36
4ENB_A	crcB links to Rfam database...	0.30	0.16	0.60	3	1270	2	0	2	0	16
4ENC_A	crcB links to Rfam database...	0.30	0.16	0.60	3	1321	2	0	2	0	16

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