CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	IPknot		Cylofold
MCC	0.586	>	0.537
Average MCC ± 95% Confidence Intervals	0.517 ± 0.153	>	0.516 ± 0.140
Sensitivity	0.474	>	0.454
Positive Predictive Value	0.732	>	0.643
Total TP	197	>	189
Total TN	42017	>	41992
Total FP	78	<	110
Total FP CONTRA	7	<	9
Total FP INCONS	65	<	96
Total FP COMP	6	>	5
Total FN	219	<	227
P-value	3.02344513449e-08

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

Total Scores
MCC	0.586
Average MCC ± 95% Confidence Intervals	0.517 ± 0.153
Sensitivity	0.474
Positive Predictive Value	0.732
Nr of predictions	15

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...	0.40	0.30	0.55	6	1529	5	1	4	0	14
2LKR_A	-	0.84	0.77	0.91	30	6072	4	0	3	1	9
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3J0L_2	-	0.39	0.36	0.43	12	6188	18	2	14	2	21
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_a	-	0.21	0.19	0.25	3	1116	9	1	8	0	13
3J0L_7	-	-0.01	0.00	0.00	0	1218	7	0	7	0	17
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.61	0.48	0.80	20	3891	5	0	5	0	22
3U4M_B	-	0.68	0.54	0.87	20	3137	3	1	2	0	17
3UZL_B	tRNA links to Rfam database...	0.72	0.54	0.95	20	3549	1	0	1	0	17
4AOB_A	SAM links to Rfam database...	0.42	0.33	0.54	14	4345	13	1	11	1	28
4ENB_A	crcB links to Rfam database...	0.76	0.58	1.00	11	1264	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.52	0.42	0.67	8	1314	4	0	4	0	11

Total Scores
MCC	0.537
Average MCC ± 95% Confidence Intervals	0.516 ± 0.140
Sensitivity	0.454
Positive Predictive Value	0.643
Nr of predictions	15

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...	0.61	0.55	0.69	11	1524	5	0	5	0	9
2LKR_A	-	0.50	0.44	0.59	17	6076	12	2	10	0	22
3AMU_B	tRNA links to Rfam database...	0.67	0.59	0.76	16	2982	7	0	5	2	11
3J0L_2	-	0.39	0.36	0.43	12	6188	18	2	14	2	21
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J0L_a	-	0.22	0.19	0.27	3	1117	8	1	7	0	13
3J0L_7	-	0.30	0.29	0.33	5	1210	10	0	10	0	12
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.62	0.50	0.78	21	3889	6	0	6	0	21
3U4M_B	-	0.38	0.32	0.46	12	3134	14	0	14	0	25
3UZL_B	tRNA links to Rfam database...	0.45	0.38	0.54	14	3544	12	1	11	0	23
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4

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