CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNAwolf		RDfolder
MCC	0.466	>	0.403
Average MCC ± 95% Confidence Intervals	0.406 ± 0.134	>	0.361 ± 0.158
Sensitivity	0.429	>	0.302
Positive Predictive Value	0.518	<	0.550
Total TP	172	>	121
Total TN	35349	<	35461
Total FP	167	>	103
Total FP CONTRA	13	>	8
Total FP INCONS	147	>	91
Total FP COMP	7	>	4
Total FN	229	<	280
P-value	2.76499031155e-08

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

Total Scores
MCC	0.466
Average MCC ± 95% Confidence Intervals	0.406 ± 0.134
Sensitivity	0.429
Positive Predictive Value	0.518
Nr of predictions	16

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
3AMU_B	tRNA links to Rfam database...	0.68	0.63	0.74	17	2980	9	0	6	3	10
3J0L_7	-	-0.01	0.00	0.00	0	1214	11	0	11	0	17
3J0L_a	-	0.18	0.19	0.20	3	1113	12	1	11	0	13
3J0L_g	-	0.16	0.25	0.11	1	456	8	6	2	0	3
3J16_L	tRNA links to Rfam database...	0.45	0.40	0.52	12	2752	11	0	11	0	18
3J20_0	tRNA links to Rfam database...	0.40	0.40	0.41	12	2821	18	0	17	1	18
3J3D_C	tRNA links to Rfam database...	0.79	0.75	0.84	21	2750	5	2	2	1	7
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
3W3S_B	tRNA-Sec links to Rfam database...	0.68	0.63	0.74	25	4719	10	0	9	1	15
4AOB_A	SAM links to Rfam database...	0.23	0.19	0.30	8	4344	20	1	18	1	34
4ATO_G	-	-0.02	0.00	0.00	0	520	8	1	7	0	10
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
4JRC_A	-	0.58	0.52	0.67	12	1522	6	0	6	0	11

Total Scores
MCC	0.403
Average MCC ± 95% Confidence Intervals	0.361 ± 0.158
Sensitivity	0.302
Positive Predictive Value	0.550
Nr of predictions	16

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...	-0.01	0.00	0.00	0	1526	14	2	12	0	20
3AMU_B	tRNA links to Rfam database...	0.18	0.15	0.22	4	2985	16	2	12	2	23
3J0L_7	-	-0.01	0.00	0.00	0	1220	5	0	5	0	17
3J0L_a	-	-0.01	0.00	0.00	0	1124	4	1	3	0	16
3J0L_g	-	-0.01	0.00	0.00	0	462	3	1	2	0	4
3J16_L	tRNA links to Rfam database...	0.22	0.17	0.31	5	2759	11	0	11	0	25
3J20_0	tRNA links to Rfam database...	0.73	0.57	0.94	17	2832	2	0	1	1	13
3J3D_C	tRNA links to Rfam database...	0.72	0.61	0.85	17	2755	3	0	3	0	11
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...	0.30	0.17	0.54	7	3903	6	0	6	0	35
3W3S_B	tRNA-Sec links to Rfam database...	0.27	0.23	0.33	9	4726	18	1	17	0	31
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ATO_G	-	0.63	0.40	1.00	4	524	0	0	0	0	6
4ENB_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1265	4	0	4	0	13
4ENC_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1316	4	0	4	0	13
4JRC_A	-	0.81	0.65	1.00	15	1525	0	0	0	0	8

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