CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	MXScarna(20)		PPfold(seed)
MCC	0.600	>	0.073
Average MCC ± 95% Confidence Intervals	0.583 ± 0.167	>	0.036 ± 0.043
Sensitivity	0.568	>	0.019
Positive Predictive Value	0.642	>	0.294
Total TP	147	>	5
Total TN	25357	<	25569
Total FP	128	>	77
Total FP CONTRA	36	>	0
Total FP INCONS	46	>	12
Total FP COMP	46	<	65
Total FN	112	<	254
P-value	1.42300079339e-08

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

Total Scores
MCC	0.600
Average MCC ± 95% Confidence Intervals	0.583 ± 0.167
Sensitivity	0.568
Positive Predictive Value	0.642
Nr of predictions	12

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.93	0.90	0.95	19	1199	1	1	0	0	2
3J3D_C	tRNA links to Rfam database...	0.90	0.95	0.86	18	947	3	3	0	0	1
3J3E_8	5_8S_rRNA links to Rfam database...	0.21	0.20	0.23	3	2729	15	4	6	5	12
3J3F_8	5_8S_rRNA links to Rfam database...	0.48	0.53	0.43	10	4738	29	7	6	16	9
3RKF_A	Purine links to Rfam database...	0.86	0.75	1.00	18	848	0	0	0	0	6
3SD1_A	THF links to Rfam database...	0.74	0.76	0.73	22	1503	9	6	2	1	7
3ZEX_C	5_8S_rRNA links to Rfam database...	0.35	0.31	0.41	9	5352	15	3	10	2	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.21	5	4492	36	8	11	17	15
4AOB_A	SAM links to Rfam database...	0.68	0.69	0.69	20	1408	13	2	7	4	9
4ENB_A	crcB links to Rfam database...	0.29	0.13	0.67	2	469	1	0	1	0	13
4ENC_A	crcB links to Rfam database...	0.68	0.47	1.00	7	489	0	0	0	0	8
4FRG_B	AdoCbl-variant links to Rfam database...	0.65	0.58	0.74	14	1183	6	2	3	1	10

Total Scores
MCC	0.073
Average MCC ± 95% Confidence Intervals	0.036 ± 0.043
Sensitivity	0.019
Positive Predictive Value	0.294
Nr of predictions	12

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J20_0	tRNA links to Rfam database...	0.00	0.00	0.00	0	1219	0	0	0	0	21
3J3D_C	tRNA links to Rfam database...	0.00	0.00	0.00	0	968	0	0	0	0	19
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2742	6	0	0	6	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.19	0.11	0.33	2	4755	24	0	4	20	17
3RKF_A	Purine links to Rfam database...	0.00	0.00	0.00	0	866	0	0	0	0	24
3SD1_A	THF links to Rfam database...	0.00	0.00	0.00	0	1533	0	0	0	0	29
3ZEX_C	5_8S_rRNA links to Rfam database...	0.15	0.07	0.33	2	5368	24	0	4	20	27
4A1C_2	5_8S_rRNA links to Rfam database...	0.10	0.05	0.20	1	4511	23	0	4	19	19
4AOB_A	SAM links to Rfam database...	0.00	0.00	0.00	0	1437	0	0	0	0	29
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	472	0	0	0	0	15
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	496	0	0	0	0	15
4FRG_B	AdoCbl-variant links to Rfam database...	0.00	0.00	0.00	0	1202	0	0	0	0	24

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