CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	MXScarna(seed)		RNASLOpt
MCC	0.679	>	0.560
Average MCC ± 95% Confidence Intervals	0.608 ± 0.272	>	0.582 ± 0.174
Sensitivity	0.620	>	0.526
Positive Predictive Value	0.752	>	0.608
Total TP	106	>	90
Total TN	12523	>	12516
Total FP	62	<	72
Total FP CONTRA	7	<	18
Total FP INCONS	28	<	40
Total FP COMP	27	>	14
Total FN	65	<	81
P-value	0.0

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

Total Scores
MCC	0.679
Average MCC ± 95% Confidence Intervals	0.608 ± 0.272
Sensitivity	0.620
Positive Predictive Value	0.752
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...	-0.03	0.00	0.00	0	518	12	0	10	2	18
3J16_L	tRNA links to Rfam database...	0.98	0.95	1.00	20	1139	0	0	0	0	1
3UZL_B	tRNA links to Rfam database...	0.83	0.75	0.92	12	1280	8	0	1	7	4
4A1C_3	5S_rRNA links to Rfam database...	0.92	0.92	0.92	34	2726	6	0	3	3	3
4A1C_2	5_8S_rRNA links to Rfam database...	0.45	0.40	0.50	8	4500	20	4	4	12	12
4AOB_A	SAM links to Rfam database...	0.71	0.69	0.74	20	1410	10	2	5	3	9
4ENB_A	crcB links to Rfam database...	0.54	0.40	0.75	6	464	2	0	2	0	9
4ENC_A	crcB links to Rfam database...	0.48	0.40	0.60	6	486	4	1	3	0	9

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.