CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	ContextFold		MXScarna(20)
MCC	0.617	>	0.570
Average MCC ± 95% Confidence Intervals	0.602 ± 0.134	>	0.551 ± 0.113
Sensitivity	0.499	>	0.470
Positive Predictive Value	0.767	>	0.696
Total TP	343	>	323
Total TN	110748	>	110731
Total FP	148	<	185
Total FP CONTRA	16	<	21
Total FP INCONS	88	<	120
Total FP COMP	44	=	44
Total FN	344	<	364
P-value	2.97012568641e-08

Comparison of performance of ContextFold 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 ContextFold 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 ContextFold and MXScarna(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for ContextFold 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 ContextFold and MXScarna(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	0.570
Average MCC ± 95% Confidence Intervals	0.551 ± 0.113
Sensitivity	0.470
Positive Predictive Value	0.696
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...	0.93	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
3J3D_C	tRNA links to Rfam database...	0.82	0.71	0.95	20	2754	1	0	1	0	8
3J3E_8	5_8S_rRNA links to Rfam database...	0.14	0.09	0.23	3	7490	15	2	8	5	30
3J3E_7	5S_rRNA links to Rfam database...	0.61	0.54	0.69	29	7098	13	2	11	0	25
3J3F_7	5S_rRNA links to Rfam database...	0.66	0.60	0.73	30	7219	12	1	10	1	20
3J3F_8	5_8S_rRNA links to Rfam database...	0.43	0.36	0.52	13	12221	26	2	10	14	23
3J3V_B	5S_rRNA links to Rfam database...	0.74	0.61	0.90	35	6982	4	1	3	0	22
3ZEX_D	5S_rRNA links to Rfam database...	0.68	0.63	0.74	31	6979	11	2	9	0	18
3ZEX_C	5_8S_rRNA links to Rfam database...	0.31	0.21	0.46	11	14172	13	2	11	0	41
3ZND_W	tRNA links to Rfam database...	0.37	0.35	0.40	8	2983	15	2	10	3	15
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.15	0.21	5	11757	36	2	17	17	28
4A1C_3	5S_rRNA links to Rfam database...	0.64	0.56	0.75	30	7100	11	2	8	1	24
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.