CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		Murlet(20)
MCC	0.617	>	0.564
Average MCC ± 95% Confidence Intervals	0.602 ± 0.134	>	0.540 ± 0.100
Sensitivity	0.499	>	0.418
Positive Predictive Value	0.767	>	0.765
Total TP	343	>	287
Total TN	110748	<	110820
Total FP	148	>	109
Total FP CONTRA	16	>	5
Total FP INCONS	88	>	83
Total FP COMP	44	>	21
Total FN	344	<	400
P-value	2.76499031155e-08

Comparison of performance of ContextFold and Murlet(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 ContextFold and Murlet(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 ContextFold and Murlet(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for ContextFold and Murlet(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 ContextFold and Murlet(20)).

Total Scores
MCC	0.617
Average MCC ± 95% Confidence Intervals	0.602 ± 0.134
Sensitivity	0.499
Positive Predictive Value	0.767
Nr of predictions	18

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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...	0.84	0.70	1.00	21	2829	1	0	0	1	9
3J2L_3	5S_rRNA links to Rfam database...	0.79	0.62	1.00	33	7842	2	0	0	2	20
3J3D_C	tRNA links to Rfam database...	0.73	0.61	0.89	17	2756	2	0	2	0	11
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7483	29	9	11	9	33
3J3E_7	5S_rRNA links to Rfam database...	0.72	0.56	0.94	30	7108	2	0	2	0	24
3J3F_7	5S_rRNA links to Rfam database...	0.81	0.68	0.97	34	7225	1	0	1	0	16
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.31	0.37	11	12216	29	3	16	10	25
3J3V_B	5S_rRNA links to Rfam database...	0.76	0.58	1.00	33	6988	0	0	0	0	24
3ZEX_D	5S_rRNA links to Rfam database...	0.81	0.67	0.97	33	6987	1	0	1	0	16
3ZEX_C	5_8S_rRNA links to Rfam database...	0.33	0.25	0.45	13	14167	22	1	15	6	39
3ZND_W	tRNA links to Rfam database...	0.21	0.22	0.22	5	2980	20	0	18	2	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.20	0.15	0.28	5	11763	26	0	13	13	28
4A1C_3	5S_rRNA links to Rfam database...	0.78	0.63	0.97	34	7105	1	0	1	0	20
4AOB_A	SAM links to Rfam database...	0.52	0.40	0.68	17	4346	9	1	7	1	25
4ENB_A	crcB links to Rfam database...	0.69	0.47	1.00	9	1266	0	0	0	0	10
4ENC_A	crcB links to Rfam database...	0.65	0.47	0.90	9	1316	1	1	0	0	10
4FRG_B	AdoCbl-variant links to Rfam database...	0.71	0.56	0.90	18	3466	2	1	1	0	14

Total Scores
MCC	0.564
Average MCC ± 95% Confidence Intervals	0.540 ± 0.100
Sensitivity	0.418
Positive Predictive Value	0.765
Nr of predictions	18

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_1	tRNA links to Rfam database...	0.68	0.57	0.81	13	2910	3	0	3	0	10
3J20_0	tRNA links to Rfam database...	0.58	0.47	0.74	14	2831	5	0	5	0	16
3J2L_3	5S_rRNA links to Rfam database...	0.69	0.49	0.96	26	7848	3	0	1	2	27
3J3D_C	tRNA links to Rfam database...	0.78	0.64	0.95	18	2756	1	0	1	0	10
3J3E_8	5_8S_rRNA links to Rfam database...	0.24	0.15	0.38	5	7490	13	1	7	5	28
3J3E_7	5S_rRNA links to Rfam database...	0.77	0.63	0.94	34	7104	2	0	2	0	20
3J3F_7	5S_rRNA links to Rfam database...	0.69	0.50	0.96	25	7234	1	0	1	0	25
3J3F_8	5_8S_rRNA links to Rfam database...	0.48	0.36	0.65	13	12226	10	0	7	3	23
3J3V_B	5S_rRNA links to Rfam database...	0.63	0.40	1.00	23	6998	0	0	0	0	34
3ZEX_D	5S_rRNA links to Rfam database...	0.77	0.65	0.91	32	6986	3	0	3	0	17
3ZEX_C	5_8S_rRNA links to Rfam database...	0.34	0.23	0.50	12	14172	15	1	11	3	40
3ZND_W	tRNA links to Rfam database...	0.45	0.39	0.53	9	2986	11	0	8	3	14
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.15	0.20	5	11756	24	2	18	4	28
4A1C_3	5S_rRNA links to Rfam database...	0.59	0.41	0.85	22	7114	4	0	4	0	32
4AOB_A	SAM links to Rfam database...	0.72	0.55	0.96	23	4347	2	0	1	1	19
4ENB_A	crcB links to Rfam database...	0.46	0.21	1.00	4	1271	0	0	0	0	15
4ENC_A	crcB links to Rfam database...	0.51	0.26	1.00	5	1321	0	0	0	0	14
4FRG_B	AdoCbl-variant links to Rfam database...	0.17	0.13	0.25	4	3470	12	1	11	0	28

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