CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RDfolder		MCFold
MCC	0.610	>	0.516
Average MCC ± 95% Confidence Intervals	0.601 ± 0.155	>	0.489 ± 0.111
Sensitivity	0.542	<	0.547
Positive Predictive Value	0.703	>	0.508
Total TP	225	<	227
Total TN	17741	>	17614
Total FP	97	<	240
Total FP CONTRA	22	<	43
Total FP INCONS	73	<	177
Total FP COMP	2	<	20
Total FN	190	>	188
P-value	5.10776592382e-08

Comparison of performance of RDfolder 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 RDfolder and MCFold).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for RDfolder and MCFold).
Comparison of average Matthews Correlation Coefficients (MCCs) for RDfolder 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 RDfolder and MCFold).

Total Scores
MCC	0.610
Average MCC ± 95% Confidence Intervals	0.601 ± 0.155
Sensitivity	0.542
Positive Predictive Value	0.703
Nr of predictions	22

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KFC_A	-	0.79	0.63	1.00	5	231	0	0	0	0	3
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	514	14	3	11	0	18
2RP0_A	-	0.84	0.71	1.00	5	111	0	0	0	0	2
2ZZN_D	tRNA links to Rfam database...	0.93	0.95	0.91	21	961	2	2	0	0	1
3A2K_C	tRNA links to Rfam database...	0.98	0.95	1.00	21	1087	0	0	0	0	1
3A3A_A	tRNA-Sec links to Rfam database...	0.59	0.50	0.71	15	1479	6	0	6	0	15
3GCA_A	-	0.84	0.71	1.00	5	153	0	0	0	0	2
3GX2_A	SAM links to Rfam database...	0.60	0.57	0.64	16	1424	10	2	7	1	12
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IWN_A	c-di-GMP-I links to Rfam database...	-0.01	0.00	0.00	0	1462	10	1	9	0	28
3J0L_a	-	-0.02	0.00	0.00	0	407	4	3	1	0	11
3J20_0	tRNA links to Rfam database...	0.82	0.76	0.89	16	1201	3	1	1	1	5
3J3D_C	tRNA links to Rfam database...	0.76	0.79	0.75	15	948	5	3	2	0	4
3JYV_7	tRNA links to Rfam database...	-0.02	0.00	0.00	0	1091	20	4	16	0	20
3LA5_A	Purine links to Rfam database...	0.91	0.84	1.00	21	933	0	0	0	0	4
3NKB_B	-	0.43	0.42	0.47	8	718	9	2	7	0	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...	0.35	0.24	0.54	7	1520	6	1	5	0	22
4ATO_G	-	0.75	0.57	1.00	4	216	0	0	0	0	3
4ENB_A	crcB links to Rfam database...	0.48	0.40	0.60	6	462	4	0	4	0	9
4ENC_A	crcB links to Rfam database...	0.48	0.40	0.60	6	486	4	0	4	0	9
4JRC_A	-	0.94	0.88	1.00	15	607	0	0	0	0	2

Total Scores
MCC	0.516
Average MCC ± 95% Confidence Intervals	0.489 ± 0.111
Sensitivity	0.547
Positive Predictive Value	0.508
Nr of predictions	22

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KFC_A	-	0.54	0.63	0.50	5	226	5	2	3	0	3
2LC8_A	GP_knot1 links to Rfam database...	0.44	0.44	0.47	8	511	10	0	9	1	10
2RP0_A	-	0.70	0.71	0.71	5	109	2	1	1	0	2
2ZZN_D	tRNA links to Rfam database...	0.69	0.73	0.67	16	960	11	1	7	3	6
3A2K_C	tRNA links to Rfam database...	0.49	0.55	0.46	12	1082	14	3	11	0	10
3A3A_A	tRNA-Sec links to Rfam database...	0.98	0.97	1.00	29	1471	0	0	0	0	1
3GCA_A	-	-0.05	0.00	0.00	0	150	8	4	4	0	7
3GX2_A	SAM links to Rfam database...	0.58	0.61	0.57	17	1419	15	1	12	2	11
3IVN_B	Purine links to Rfam database...	0.45	0.48	0.46	11	879	14	5	8	1	12
3IWN_A	c-di-GMP-I links to Rfam database...	0.19	0.21	0.20	6	1442	24	5	19	0	22
3J0L_a	-	0.14	0.18	0.15	2	398	13	1	10	2	9
3J20_0	tRNA links to Rfam database...	0.66	0.71	0.63	15	1195	11	3	6	2	6
3J3D_C	tRNA links to Rfam database...	0.54	0.63	0.48	12	943	13	4	9	0	7
3JYV_7	tRNA links to Rfam database...	0.25	0.30	0.24	6	1086	20	8	11	1	14
3LA5_A	Purine links to Rfam database...	0.44	0.44	0.48	11	931	12	2	10	0	14
3NKB_B	-	0.68	0.74	0.64	14	713	8	2	6	0	5
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
4ATO_G	-	0.36	0.43	0.33	3	211	8	0	6	2	4
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
4JRC_A	-	0.24	0.29	0.23	5	600	17	0	17	0	12

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