CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(20)		Vsfold4
MCC	0.581	>	0.544
Average MCC ± 95% Confidence Intervals	0.583 ± 0.267	<	0.604 ± 0.295
Sensitivity	0.576	>	0.523
Positive Predictive Value	0.598	>	0.580
Total TP	76	>	69
Total TN	9193	<	9201
Total FP	60	<	63
Total FP CONTRA	17	>	12
Total FP INCONS	34	<	38
Total FP COMP	9	<	13
Total FN	56	<	63
P-value	0.0

Comparison of performance of Multilign(20) and Vsfold4. 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 Multilign(20) and Vsfold4).
Comparison of average Matthews Correlation Coefficients (MCCs) for Multilign(20) and Vsfold4. 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 Multilign(20) and Vsfold4).

Total Scores
MCC	0.581
Average MCC ± 95% Confidence Intervals	0.583 ± 0.267
Sensitivity	0.576
Positive Predictive Value	0.598
Nr of predictions	6

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3RKF_A	Purine links to Rfam database...	0.91	0.88	0.95	21	844	1	0	1	0	3
3SD1_A	THF links to Rfam database...	0.68	0.69	0.69	20	1504	9	4	5	0	9
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.25	0.16	5	4485	33	9	17	7	15
4AOB_A	SAM links to Rfam database...	0.59	0.55	0.64	16	1412	10	3	6	1	13
4ENB_A	crcB links to Rfam database...	0.39	0.33	0.50	5	462	6	0	5	1	10
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6

Total Scores
MCC	0.544
Average MCC ± 95% Confidence Intervals	0.604 ± 0.295
Sensitivity	0.523
Positive Predictive Value	0.580
Nr of predictions	6

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.23	0.24	0.24	7	1504	22	5	17	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.36	0.40	0.33	8	4492	28	4	12	12	12
4AOB_A	SAM links to Rfam database...	0.50	0.48	0.54	14	1411	13	3	9	1	15
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...	0.77	0.60	1.00	9	487	0	0	0	0	6

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