CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		Vsfold5
MCC	0.601	>	0.340
Average MCC ± 95% Confidence Intervals	0.543 ± 0.159	>	0.340 ± 0.179
Sensitivity	0.483	>	0.295
Positive Predictive Value	0.754	>	0.401
Total TP	193	>	118
Total TN	51821	>	51783
Total FP	81	<	191
Total FP CONTRA	5	<	16
Total FP INCONS	58	<	160
Total FP COMP	18	>	15
Total FN	207	<	282
P-value	1.79203144115e-08

Comparison of performance of ContextFold and Vsfold5. 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 ContextFold and Vsfold5).
Comparison of average Matthews Correlation Coefficients (MCCs) for ContextFold and Vsfold5. 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 ContextFold and Vsfold5).

Total Scores
MCC	0.601
Average MCC ± 95% Confidence Intervals	0.543 ± 0.159
Sensitivity	0.483
Positive Predictive Value	0.754
Nr of predictions	14

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...	0.55	0.50	0.63	10	1524	6	0	6	0	10
2LKR_A	-	0.65	0.56	0.76	22	6076	9	0	7	2	17
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J0L_2	-	0.64	0.61	0.69	20	6187	11	2	7	2	13
3J0L_g	-	-0.01	0.00	0.00	0	462	3	1	2	0	4
3J0L_a	-	0.71	0.56	0.90	9	1118	1	0	1	0	7
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3U4M_B	-	0.75	0.57	1.00	21	3139	0	0	0	0	16
3UZL_B	tRNA links to Rfam database...	0.72	0.54	0.95	20	3549	1	0	1	0	17
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.15	0.28	5	11763	26	0	13	13	28
4A1C_3	5S_rRNA links to Rfam database...	0.78	0.63	0.97	34	7105	1	0	1	0	20
4AOB_A	SAM links to Rfam database...	0.52	0.40	0.68	17	4346	9	1	7	1	25
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10

Total Scores
MCC	0.340
Average MCC ± 95% Confidence Intervals	0.340 ± 0.179
Sensitivity	0.295
Positive Predictive Value	0.401
Nr of predictions	14

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
2LKR_A	-	0.27	0.23	0.32	9	6077	19	2	17	0	30
3J0L_7	-	-0.01	0.00	0.00	0	1212	13	0	13	0	17
3J0L_2	-	0.35	0.33	0.37	11	6186	21	3	16	2	22
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_a	-	0.39	0.31	0.50	5	1118	5	2	3	0	11
3J16_L	tRNA links to Rfam database...	0.82	0.67	1.00	20	2755	0	0	0	0	10
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3UZL_B	tRNA links to Rfam database...	0.16	0.14	0.20	5	3545	20	1	19	0	32
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.24	0.24	8	11748	37	3	22	12	25
4A1C_3	5S_rRNA links to Rfam database...	0.26	0.22	0.32	12	7103	25	2	23	0	42
4AOB_A	SAM links to Rfam database...	0.18	0.14	0.25	6	4347	19	1	17	1	36
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4

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