CompaRNA - on-line benchmarks of RNA structure prediction methods

FAQ

Metric	MXScarna(20)		CMfinder(20)
MCC	0.600	>	0.521
Average MCC ± 95% Confidence Intervals	0.578 ± 0.137	>	0.514 ± 0.127
Sensitivity	0.506	>	0.366
Positive Predictive Value	0.717	<	0.748
Total TP	225	>	163
Total TN	67866	<	67962
Total FP	114	>	61
Total FP CONTRA	15	>	4
Total FP INCONS	74	>	51
Total FP COMP	25	>	6
Total FN	220	<	282
P-value	1.39551335374e-08

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

Total Scores
MCC	0.600
Average MCC ± 95% Confidence Intervals	0.578 ± 0.137
Sensitivity	0.506
Positive Predictive Value	0.717
Nr of predictions	11

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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_8	5_8S_rRNA links to Rfam database...	0.43	0.36	0.52	13	12221	26	2	10	14	23
3J3F_7	5S_rRNA links to Rfam database...	0.66	0.60	0.73	30	7219	12	1	10	1	20
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
3ZND_W	tRNA links to Rfam database...	0.37	0.35	0.40	8	2983	15	2	10	3	15
4FRG_B	AdoCbl-variant links to Rfam database...	0.55	0.44	0.70	14	3466	6	2	4	0	18

Total Scores
MCC	0.521
Average MCC ± 95% Confidence Intervals	0.514 ± 0.127
Sensitivity	0.366
Positive Predictive Value	0.748
Nr of predictions	11

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.75	0.57	1.00	17	2833	1	0	0	1	13
3J2L_3	5S_rRNA links to Rfam database...	0.45	0.32	0.63	17	7848	11	1	9	1	36
3J3D_C	tRNA links to Rfam database...	0.76	0.61	0.94	17	2757	1	0	1	0	11
3J3E_8	5_8S_rRNA links to Rfam database...	0.10	0.06	0.17	2	7491	10	1	9	0	31
3J3E_7	5S_rRNA links to Rfam database...	0.62	0.46	0.83	25	7110	5	1	4	0	29
3J3F_8	5_8S_rRNA links to Rfam database...	0.45	0.33	0.60	12	12226	8	1	7	0	24
3J3F_7	5S_rRNA links to Rfam database...	0.66	0.52	0.84	26	7229	6	0	5	1	24
3J3V_B	5S_rRNA links to Rfam database...	0.38	0.21	0.71	12	7004	5	0	5	0	45
3ZEX_D	5S_rRNA links to Rfam database...	0.58	0.39	0.86	19	6999	3	0	3	0	30
3ZND_W	tRNA links to Rfam database...	0.45	0.39	0.53	9	2986	11	0	8	3	14
4FRG_B	AdoCbl-variant links to Rfam database...	0.47	0.22	1.00	7	3479	0	0	0	0	25

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