CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	IPknot		RNAwolf
MCC	0.567	>	0.399
Average MCC ± 95% Confidence Intervals	0.507 ± 0.142	>	0.380 ± 0.128
Sensitivity	0.463	>	0.368
Positive Predictive Value	0.702	>	0.444
Total TP	233	>	185
Total TN	60875	>	60790
Total FP	110	<	253
Total FP CONTRA	12	<	28
Total FP INCONS	87	<	204
Total FP COMP	11	<	21
Total FN	270	<	318
P-value	2.8150742666e-08

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

Total Scores
MCC	0.567
Average MCC ± 95% Confidence Intervals	0.507 ± 0.142
Sensitivity	0.463
Positive Predictive Value	0.702
Nr of predictions	17

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_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_2	-	0.39	0.36	0.43	12	6188	18	2	14	2	21
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
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	11755	26	4	17	5	28
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	1	5	0	23
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	0.399
Average MCC ± 95% Confidence Intervals	0.380 ± 0.128
Sensitivity	0.368
Positive Predictive Value	0.444
Nr of predictions	17

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...	0.52	0.50	0.56	10	1522	8	0	8	0	10
2LKR_A	-	0.81	0.74	0.88	29	6072	8	0	4	4	10
3AMU_B	tRNA links to Rfam database...	0.68	0.63	0.74	17	2980	9	0	6	3	10
3J0L_g	-	0.16	0.25	0.11	1	456	8	6	2	0	3
3J0L_a	-	0.18	0.19	0.20	3	1113	12	1	11	0	13
3J0L_2	-	0.11	0.12	0.11	4	6181	34	5	26	3	29
3J0L_7	-	-0.01	0.00	0.00	0	1214	11	0	11	0	17
3J16_L	tRNA links to Rfam database...	0.45	0.40	0.52	12	2752	11	0	11	0	18
3RKF_A	Purine links to Rfam database...	0.72	0.62	0.84	21	2186	4	0	4	0	13
3SD1_A	THF links to Rfam database...	0.46	0.43	0.50	18	3880	18	0	18	0	24
3U4M_B	-	0.44	0.38	0.52	14	3133	13	0	13	0	23
3UZL_B	tRNA links to Rfam database...	0.72	0.59	0.88	22	3545	4	1	2	1	15
4A1C_2	5_8S_rRNA links to Rfam database...	0.08	0.09	0.08	3	11741	46	10	27	9	30
4A1C_3	5S_rRNA links to Rfam database...	0.23	0.20	0.28	11	7101	28	2	26	0	43
4AOB_A	SAM links to Rfam database...	0.23	0.19	0.30	8	4344	20	1	18	1	34
4ENB_A	crcB links to Rfam database...	0.35	0.32	0.40	6	1260	9	1	8	0	13
4ENC_A	crcB links to Rfam database...	0.34	0.32	0.38	6	1310	10	1	9	0	13

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