CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	Cylofold		PknotsRG
MCC	0.693	>	0.682
Average MCC ± 95% Confidence Intervals	0.672 ± 0.157	<	0.673 ± 0.155
Sensitivity	0.681	<	0.694
Positive Predictive Value	0.715	>	0.680
Total TP	211	<	215
Total TN	20906	>	20885
Total FP	106	<	127
Total FP CONTRA	27	<	30
Total FP INCONS	57	<	71
Total FP COMP	22	<	26
Total FN	99	>	95
P-value	3.73294613682e-07

Comparison of performance of Cylofold and PknotsRG. 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 Cylofold and PknotsRG).
Comparison of average Matthews Correlation Coefficients (MCCs) for Cylofold and PknotsRG. 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 Cylofold and PknotsRG).

Total Scores
MCC	0.693
Average MCC ± 95% Confidence Intervals	0.672 ± 0.157
Sensitivity	0.681
Positive Predictive Value	0.715
Nr of predictions	13

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.85	0.87	0.83	20	2000	12	4	0	8	3
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	5	1	4	0	7
3ADB_C	-	0.84	0.82	0.87	27	1788	4	0	4	0	6
3J0L_a	-	0.17	0.18	0.20	2	401	9	3	5	1	9
3NKB_B	-	0.46	0.42	0.53	8	720	7	0	7	0	11
3O58_3	5_8S_rRNA links to Rfam database...	0.42	0.50	0.35	11	4733	30	9	11	10	11
3PDR_A	ykoK links to Rfam database...	0.86	0.78	0.95	39	4799	4	1	1	2	11
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...	0.71	0.69	0.74	20	1506	7	2	5	0	9
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
4AOB_A	SAM links to Rfam database...	0.42	0.38	0.48	11	1414	13	3	9	1	18
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0

Total Scores
MCC	0.682
Average MCC ± 95% Confidence Intervals	0.673 ± 0.155
Sensitivity	0.694
Positive Predictive Value	0.680
Nr of predictions	13

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KRL_A	-	0.85	0.87	0.83	20	2000	12	4	0	8	3
2LC8_A	GP_knot1 links to Rfam database...	0.66	0.61	0.73	11	513	4	2	2	0	7
3ADB_C	-	0.35	0.36	0.36	12	1786	21	1	20	0	21
3J0L_a	-	0.18	0.18	0.22	2	402	8	3	4	1	9
3NKB_B	-	0.69	0.74	0.67	14	714	7	0	7	0	5
3O58_3	5_8S_rRNA links to Rfam database...	0.41	0.50	0.34	11	4732	35	6	15	14	11
3PDR_A	ykoK links to Rfam database...	0.90	0.90	0.90	45	4790	7	2	3	2	5
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...	0.73	0.72	0.75	21	1505	7	4	3	0	8
3U4M_B	-	0.49	0.55	0.46	12	1250	14	3	11	0	10
4AOB_A	SAM links to Rfam database...	0.60	0.59	0.63	17	1410	11	4	6	1	12
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0

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