CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidAlifold(20)		Murlet(seed)
MCC	0.650	>	0.490
Average MCC ± 95% Confidence Intervals	0.622 ± 0.086	>	0.492 ± 0.051
Sensitivity	0.470	>	0.269
Positive Predictive Value	0.904	>	0.899
Total TP	264	>	151
Total TN	89041	<	89165
Total FP	46	>	23
Total FP CONTRA	3	<	5
Total FP INCONS	25	>	12
Total FP COMP	18	>	6
Total FN	298	<	411
P-value	2.52609899389e-08

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

Total Scores
MCC	0.650
Average MCC ± 95% Confidence Intervals	0.622 ± 0.086
Sensitivity	0.470
Positive Predictive Value	0.904
Nr of predictions	16

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.61	0.55	0.69	11	974	5	0	5	0	9
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.46	0.25	0.83	5	4554	6	0	1	5	15
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.44	0.19	1.00	8	5143	3	0	0	3	34
3GX2_A	SAM links to Rfam database...	0.77	0.60	1.00	24	4347	1	0	0	1	16
3IVN_B	Purine links to Rfam database...	0.78	0.65	0.95	20	2325	1	1	0	0	11
3JYX_4	5_8S_rRNA links to Rfam database...	0.39	0.27	0.56	9	12230	9	0	7	2	24
3LA5_A	Purine links to Rfam database...	0.78	0.62	1.00	21	2464	0	0	0	0	13
3NPB_A	SAM links to Rfam database...	0.70	0.54	0.89	25	6993	5	1	2	2	21
3O58_3	5_8S_rRNA links to Rfam database...	0.54	0.31	0.92	11	12391	1	0	1	0	24
3PDR_A	ykoK links to Rfam database...	0.76	0.63	0.94	45	12832	5	0	3	2	27
3RKF_A	Purine links to Rfam database...	0.72	0.53	1.00	18	2193	0	0	0	0	16
3SD1_A	THF links to Rfam database...	0.71	0.52	0.96	22	3893	1	0	1	0	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.26	0.15	0.45	5	11770	8	1	5	2	28
4AOB_A	SAM links to Rfam database...	0.75	0.57	1.00	24	4347	1	0	0	1	18
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...	0.60	0.37	1.00	7	1319	0	0	0	0	12

Total Scores
MCC	0.490
Average MCC ± 95% Confidence Intervals	0.492 ± 0.051
Sensitivity	0.269
Positive Predictive Value	0.899
Nr of predictions	16

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	0.59	0.40	0.89	8	981	1	0	1	0	12
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.45	0.20	1.00	4	4556	2	0	0	2	16
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.38	0.14	1.00	6	5145	0	0	0	0	36
3GX2_A	SAM links to Rfam database...	0.59	0.35	1.00	14	4357	1	0	0	1	26
3IVN_B	Purine links to Rfam database...	0.53	0.39	0.75	12	2330	4	2	2	0	19
3JYX_4	5_8S_rRNA links to Rfam database...	0.23	0.09	0.60	3	12241	4	0	2	2	30
3LA5_A	Purine links to Rfam database...	0.58	0.41	0.82	14	2468	3	1	2	0	20
3NPB_A	SAM links to Rfam database...	0.49	0.28	0.87	13	7006	2	1	1	0	33
3O58_3	5_8S_rRNA links to Rfam database...	0.45	0.20	1.00	7	12396	0	0	0	0	28
3PDR_A	ykoK links to Rfam database...	0.44	0.19	1.00	14	12866	0	0	0	0	58
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
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

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