CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	IPknot		MCFold
MCC	0.633	>	0.500
Average MCC ± 95% Confidence Intervals	0.599 ± 0.253	>	0.493 ± 0.234
Sensitivity	0.597	>	0.532
Positive Predictive Value	0.681	>	0.485
Total TP	92	>	82
Total TN	9963	>	9929
Total FP	53	<	113
Total FP CONTRA	14	<	15
Total FP INCONS	29	<	72
Total FP COMP	10	<	26
Total FN	62	<	72
P-value	0.0

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

Total Scores
MCC	0.633
Average MCC ± 95% Confidence Intervals	0.599 ± 0.253
Sensitivity	0.597
Positive Predictive Value	0.681
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...	0.41	0.33	0.55	6	517	5	1	4	0	12
3J0L_a	-	0.16	0.18	0.18	2	400	10	3	6	1	9
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...	0.74	0.69	0.80	20	1508	5	0	5	0	9
3U4M_B	-	0.91	0.91	0.91	20	1254	3	2	0	1	2
4A1C_2	5_8S_rRNA links to Rfam database...	0.23	0.25	0.22	5	4493	26	8	10	8	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...	0.59	0.53	0.67	8	484	4	0	4	0	7

Total Scores
MCC	0.500
Average MCC ± 95% Confidence Intervals	0.493 ± 0.234
Sensitivity	0.532
Positive Predictive Value	0.485
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...	0.44	0.44	0.47	8	511	10	0	9	1	10
3J0L_a	-	0.14	0.18	0.15	2	398	13	1	10	2	9
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
3U4M_B	-	0.74	0.77	0.71	17	1252	10	1	6	3	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.25	0.14	5	4480	45	12	19	14	15
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.