CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	IPknot		RDfolder
MCC	0.555	>	0.403
Average MCC ± 95% Confidence Intervals	0.484 ± 0.139	>	0.361 ± 0.158
Sensitivity	0.444	>	0.302
Positive Predictive Value	0.704	>	0.550
Total TP	178	>	121
Total TN	35428	<	35461
Total FP	81	<	103
Total FP CONTRA	4	<	8
Total FP INCONS	71	<	91
Total FP COMP	6	>	4
Total FN	223	<	280
P-value	2.12160100812e-08

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

Total Scores
MCC	0.555
Average MCC ± 95% Confidence Intervals	0.484 ± 0.139
Sensitivity	0.444
Positive Predictive Value	0.704
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...	0.40	0.30	0.55	6	1529	5	1	4	0	14
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3J0L_7	-	-0.01	0.00	0.00	0	1218	7	0	7	0	17
3J0L_a	-	0.21	0.19	0.25	3	1116	9	1	8	0	13
3J0L_g	-	-0.01	0.00	0.00	0	461	4	1	3	0	4
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3J20_0	tRNA links to Rfam database...	0.45	0.40	0.52	12	2827	12	0	11	1	18
3J3D_C	tRNA links to Rfam database...	0.52	0.43	0.63	12	2756	7	0	7	0	16
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
3W3S_B	tRNA-Sec links to Rfam database...	0.85	0.75	0.97	30	4722	2	0	1	1	10
4AOB_A	SAM links to Rfam database...	0.42	0.33	0.54	14	4345	13	1	11	1	28
4ATO_G	-	0.41	0.40	0.44	4	519	6	0	5	1	6
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
4JRC_A	-	0.39	0.22	0.71	5	1533	2	0	2	0	18

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.