CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	MCFold		Fold
MCC	0.544	>	0.530
Average MCC ± 95% Confidence Intervals	0.516 ± 0.179	>	0.449 ± 0.204
Sensitivity	0.588	>	0.551
Positive Predictive Value	0.514	<	0.521
Total TP	144	>	135
Total TN	20157	<	20178
Total FP	174	>	159
Total FP CONTRA	36	<	38
Total FP INCONS	100	>	86
Total FP COMP	38	>	35
Total FN	101	<	110
P-value	0.0318548130709

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

Total Scores
MCC	0.544
Average MCC ± 95% Confidence Intervals	0.516 ± 0.179
Sensitivity	0.588
Positive Predictive Value	0.514
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...	0.44	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
3NKB_B	-	0.68	0.74	0.64	14	713	8	2	6	0	5
3O58_3	5_8S_rRNA links to Rfam database...	0.28	0.36	0.22	8	4727	39	14	15	10	14
3PDR_A	ykoK links to Rfam database...	0.78	0.80	0.77	40	4788	14	5	7	2	10
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

Total Scores
MCC	0.530
Average MCC ± 95% Confidence Intervals	0.449 ± 0.204
Sensitivity	0.551
Positive Predictive Value	0.521
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...	-0.03	0.00	0.00	0	513	15	3	12	0	18
3J0L_a	-	0.15	0.18	0.17	2	399	11	4	6	1	9
3NKB_B	-	0.41	0.42	0.42	8	716	11	4	7	0	11
3O58_3	5_8S_rRNA links to Rfam database...	0.39	0.50	0.31	11	4728	41	9	16	16	11
3PDR_A	ykoK links to Rfam database...	0.93	0.92	0.94	46	4791	5	1	2	2	4
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...	0.68	0.69	0.69	20	1504	9	4	5	0	9
3U4M_B	-	0.58	0.59	0.59	13	1254	9	2	7	0	9
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.15	5	4482	43	11	18	14	15
4ENB_A	crcB links to Rfam database...	0.37	0.33	0.45	5	461	7	0	6	1	10
4ENC_A	crcB links to Rfam database...	0.36	0.33	0.42	5	484	8	0	7	1	10

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