CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	IPknot		Afold
MCC	0.442	>	0.394
Average MCC ± 95% Confidence Intervals	0.565 ± 0.214	>	0.477 ± 0.156
Sensitivity	0.384	<	0.429
Positive Predictive Value	0.510	>	0.363
Total TP	203	<	227
Total TN	434729	>	434501
Total FP	230	<	475
Total FP CONTRA	43	<	107
Total FP INCONS	152	<	292
Total FP COMP	35	<	76
Total FN	326	>	302
P-value	1.62930789924e-09

Comparison of performance of IPknot and Afold. 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 IPknot and Afold).
Comparison of average Matthews Correlation Coefficients (MCCs) for IPknot and Afold. 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 IPknot and Afold).

Total Scores
MCC	0.442
Average MCC ± 95% Confidence Intervals	0.565 ± 0.214
Sensitivity	0.384
Positive Predictive Value	0.510
Nr of predictions	11

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...	0.41	0.33	0.55	6	517	5	1	4	0	12
2M58_A	-	0.71	0.58	0.88	7	536	1	1	0	0	5
3J3E_8	5_8S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	2723	25	5	14	6	15
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3U4M_B	-	0.91	0.91	0.91	20	1254	3	2	0	1	2
3W3S_B	tRNA-Sec links to Rfam database...	0.94	0.91	0.97	30	1958	2	0	1	1	3
3ZEX_B	-	0.33	0.27	0.40	95	421115	160	26	116	18	251
4A1C_2	5_8S_rRNA links to Rfam database...	0.23	0.25	0.22	5	4493	26	8	10	8	15
4ATO_G	-	0.49	0.57	0.44	4	211	6	0	5	1	3
4ENB_A	crcB links to Rfam database...	0.85	0.73	1.00	11	461	0	0	0	0	4
4JRC_A	-	0.45	0.29	0.71	5	615	2	0	2	0	12

Total Scores
MCC	0.394
Average MCC ± 95% Confidence Intervals	0.477 ± 0.156
Sensitivity	0.429
Positive Predictive Value	0.363
Nr of predictions	11

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...	0.64	0.61	0.69	11	512	6	0	5	1	7
2M58_A	-	0.40	0.42	0.42	5	532	8	1	6	1	7
3J3E_8	5_8S_rRNA links to Rfam database...	0.26	0.33	0.21	5	2718	31	6	13	12	10
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
3W3S_B	tRNA-Sec links to Rfam database...	0.55	0.55	0.56	18	1957	15	4	10	1	15
3ZEX_B	-	0.34	0.38	0.31	132	420926	337	77	217	43	214
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4483	43	11	17	15	15
4ATO_G	-	0.38	0.43	0.38	3	212	6	5	0	1	4
4ENB_A	crcB links to Rfam database...	0.81	0.73	0.92	11	460	3	0	1	2	4
4JRC_A	-	0.27	0.29	0.29	5	605	12	0	12	0	12

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