CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	IPknot		MXScarna(20)
MCC	0.601	>	0.596
Average MCC ± 95% Confidence Intervals	0.609 ± 0.114	>	0.597 ± 0.128
Sensitivity	0.485	>	0.483
Positive Predictive Value	0.751	>	0.741
Total TP	247	>	246
Total TN	73048	>	73045
Total FP	96	<	109
Total FP CONTRA	8	<	13
Total FP INCONS	74	>	73
Total FP COMP	14	<	23
Total FN	262	<	263
P-value	0.115206966267

Comparison of performance of IPknot and MXScarna(20). 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 MXScarna(20)).
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 MXScarna(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for IPknot and MXScarna(20). 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 MXScarna(20)).

Total Scores
MCC	0.601
Average MCC ± 95% Confidence Intervals	0.609 ± 0.114
Sensitivity	0.485
Positive Predictive Value	0.751
Nr of predictions	14

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.70	0.59	0.84	16	2984	5	0	3	2	11
3J20_1	tRNA links to Rfam database...	0.96	0.91	1.00	21	2905	0	0	0	0	2
3J20_0	tRNA links to Rfam database...	0.45	0.40	0.52	12	2827	12	0	11	1	18
3J2L_3	5S_rRNA links to Rfam database...	0.66	0.55	0.81	29	7839	9	0	7	2	24
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
3ZEX_C	5_8S_rRNA links to Rfam database...	0.41	0.21	0.79	11	14182	6	1	2	3	41
3ZEX_D	5S_rRNA links to Rfam database...	0.72	0.63	0.82	31	6983	7	0	7	0	18
4A1C_3	5S_rRNA links to Rfam database...	0.69	0.57	0.84	31	7103	6	1	5	0	23
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.15	0.19	5	11755	26	4	17	5	28
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
4FRG_B	AdoCbl-variant links to Rfam database...	0.69	0.56	0.86	18	3465	3	1	2	0	14

Total Scores
MCC	0.596
Average MCC ± 95% Confidence Intervals	0.597 ± 0.128
Sensitivity	0.483
Positive Predictive Value	0.741
Nr of predictions	14

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3AMU_B	tRNA links to Rfam database...	0.86	0.74	1.00	20	2983	2	0	0	2	7
3J20_1	tRNA links to Rfam database...	0.93	0.87	1.00	20	2906	0	0	0	0	3
3J20_0	tRNA links to Rfam database...	0.82	0.67	1.00	20	2830	0	0	0	0	10
3J2L_3	5S_rRNA links to Rfam database...	0.54	0.42	0.71	22	7844	11	1	8	2	31
3RKF_A	Purine links to Rfam database...	0.72	0.53	1.00	18	2193	0	0	0	0	16
3SD1_A	THF links to Rfam database...	0.63	0.55	0.74	23	3885	8	2	6	0	19
3ZEX_C	5_8S_rRNA links to Rfam database...	0.31	0.21	0.46	11	14172	13	2	11	0	41
3ZEX_D	5S_rRNA links to Rfam database...	0.68	0.63	0.74	31	6979	11	2	9	0	18
4A1C_3	5S_rRNA links to Rfam database...	0.64	0.56	0.75	30	7100	11	2	8	1	24
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.15	0.21	5	11757	36	2	17	17	28
4AOB_A	SAM links to Rfam database...	0.62	0.55	0.72	23	4339	10	0	9	1	19
4ENB_A	crcB links to Rfam database...	0.26	0.11	0.67	2	1272	1	0	1	0	17
4ENC_A	crcB links to Rfam database...	0.60	0.37	1.00	7	1319	0	0	0	0	12
4FRG_B	AdoCbl-variant links to Rfam database...	0.55	0.44	0.70	14	3466	6	2	4	0	18

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