CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASLOpt		RNAsubopt
MCC	0.449	>	0.402
Average MCC ± 95% Confidence Intervals	0.484 ± 0.218	>	0.404 ± 0.267
Sensitivity	0.438	>	0.423
Positive Predictive Value	0.475	>	0.399
Total TP	57	>	55
Total TN	9016	>	8998
Total FP	73	<	100
Total FP CONTRA	23	<	26
Total FP INCONS	40	<	57
Total FP COMP	10	<	17
Total FN	73	<	75
P-value	0.0

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

Total Scores
MCC	0.449
Average MCC ± 95% Confidence Intervals	0.484 ± 0.218
Sensitivity	0.438
Positive Predictive Value	0.475
Nr of predictions	7

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
3J0L_a	-	0.21	0.18	0.29	2	404	6	3	2	1	9
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	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

Total Scores
MCC	0.402
Average MCC ± 95% Confidence Intervals	0.404 ± 0.267
Sensitivity	0.423
Positive Predictive Value	0.399
Nr of predictions	7

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...	-0.03	0.00	0.00	0	513	15	3	12	0	18
3J0L_a	-	0.35	0.36	0.36	4	400	8	3	4	1	7
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.25	0.14	5	4481	43	13	17	13	15
4AOB_A	SAM links to Rfam database...	0.62	0.62	0.64	18	1409	11	4	6	1	11
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...	0.36	0.33	0.42	5	484	7	0	7	0	10

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