CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	PPfold(20)		Murlet(seed)
MCC	0.509	>	0.429
Average MCC ± 95% Confidence Intervals	0.502 ± 0.164	>	0.435 ± 0.102
Sensitivity	0.371	>	0.219
Positive Predictive Value	0.702	<	0.843
Total TP	127	>	75
Total TN	62130	<	62222
Total FP	70	>	17
Total FP CONTRA	0	<	1
Total FP INCONS	54	>	13
Total FP COMP	16	>	3
Total FN	215	<	267
P-value	1.31583660336e-08

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

Total Scores
MCC	0.509
Average MCC ± 95% Confidence Intervals	0.502 ± 0.164
Sensitivity	0.371
Positive Predictive Value	0.702
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J3E_8	5_8S_rRNA links to Rfam database...	0.14	0.09	0.23	3	7490	13	0	10	3	30
3J3F_8	5_8S_rRNA links to Rfam database...	0.33	0.25	0.43	9	12225	18	0	12	6	27
3RKF_A	Purine links to Rfam database...	0.73	0.56	0.95	19	2191	1	0	1	0	15
3SD1_A	THF links to Rfam database...	0.68	0.52	0.88	22	3891	3	0	3	0	20
3ZEX_C	5_8S_rRNA links to Rfam database...	0.33	0.21	0.52	11	14175	12	0	10	2	41
4A1C_2	5_8S_rRNA links to Rfam database...	0.21	0.15	0.29	5	11764	16	0	12	4	28
4AOB_A	SAM links to Rfam database...	0.74	0.60	0.93	25	4344	3	0	2	1	17
4ENB_A	crcB links to Rfam database...	0.56	0.37	0.88	7	1267	1	0	1	0	12
4ENC_A	crcB links to Rfam database...	0.58	0.42	0.80	8	1316	2	0	2	0	11
4FRG_B	AdoCbl-variant links to Rfam database...	0.73	0.56	0.95	18	3467	1	0	1	0	14

Total Scores
MCC	0.429
Average MCC ± 95% Confidence Intervals	0.435 ± 0.102
Sensitivity	0.219
Positive Predictive Value	0.843
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J3E_8	5_8S_rRNA links to Rfam database...	0.25	0.06	1.00	2	7501	2	0	0	2	31
3J3F_8	5_8S_rRNA links to Rfam database...	0.44	0.19	1.00	7	12239	0	0	0	0	29
3RKF_A	Purine links to Rfam database...	0.53	0.35	0.80	12	2196	3	1	2	0	22
3SD1_A	THF links to Rfam database...	0.47	0.26	0.85	11	3903	2	0	2	0	31
3ZEX_C	5_8S_rRNA links to Rfam database...	0.37	0.13	1.00	7	14189	0	0	0	0	45
4A1C_2	5_8S_rRNA links to Rfam database...	0.46	0.21	1.00	7	11774	0	0	0	0	26
4AOB_A	SAM links to Rfam database...	0.58	0.33	1.00	14	4357	1	0	0	1	28
4ENB_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1269	0	0	0	0	13
4ENC_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1320	0	0	0	0	13
4FRG_B	AdoCbl-variant links to Rfam database...	0.15	0.09	0.25	3	3474	9	0	9	0	29

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