CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Multilign(20)		MCFold
MCC	0.616	>	0.556
Average MCC ± 95% Confidence Intervals	0.610 ± 0.264	>	0.579 ± 0.237
Sensitivity	0.585	<	0.590
Positive Predictive Value	0.660	>	0.536
Total TP	124	<	125
Total TN	14017	>	13972
Total FP	78	<	135
Total FP CONTRA	16	<	18
Total FP INCONS	48	<	90
Total FP COMP	14	<	27
Total FN	88	>	87
P-value	0.0

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

Total Scores
MCC	0.616
Average MCC ± 95% Confidence Intervals	0.610 ± 0.264
Sensitivity	0.585
Positive Predictive Value	0.660
Nr of predictions	9

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2XXA_G	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	2033	12	2	10	0	35
3AMU_B	tRNA links to Rfam database...	0.71	0.74	0.70	14	1137	9	0	6	3	5
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
4A1C_3	5S_rRNA links to Rfam database...	0.88	0.86	0.89	32	2727	6	0	4	2	5
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	0.556
Average MCC ± 95% Confidence Intervals	0.579 ± 0.237
Sensitivity	0.590
Positive Predictive Value	0.536
Nr of predictions	9

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.23	0.26	0.24	9	2007	30	1	28	1	26
3AMU_B	tRNA links to Rfam database...	0.50	0.58	0.44	11	1132	15	4	10	1	8
3RKF_A	Purine links to Rfam database...	0.89	0.88	0.91	21	843	3	0	2	1	3
3SD1_A	THF links to Rfam database...	0.43	0.45	0.43	13	1503	17	1	16	0	16
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.25	0.14	5	4480	45	12	19	14	15
4A1C_3	5S_rRNA links to Rfam database...	0.86	0.86	0.86	32	2726	9	0	5	4	5
4ENB_A	crcB links to Rfam database...	0.78	0.73	0.85	11	459	4	0	2	2	4
4ENC_A	crcB links to Rfam database...	0.34	0.33	0.38	5	483	11	0	8	3	10

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