CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNAalifold(seed)		RNASampler(20)
MCC	0.670	>	0.647
Average MCC ± 95% Confidence Intervals	0.644 ± 0.108	<	0.652 ± 0.123
Sensitivity	0.487	<	0.569
Positive Predictive Value	0.927	>	0.742
Total TP	243	<	284
Total TN	63861	>	63740
Total FP	35	<	157
Total FP CONTRA	12	<	38
Total FP INCONS	7	<	61
Total FP COMP	16	<	58
Total FN	256	>	215
P-value	2.9966815982e-08

Comparison of performance of RNAalifold(seed) and RNASampler(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 RNAalifold(seed) and RNASampler(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 RNAalifold(seed) and RNASampler(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAalifold(seed) and RNASampler(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 RNAalifold(seed) and RNASampler(20)).

Total Scores
MCC	0.670
Average MCC ± 95% Confidence Intervals	0.644 ± 0.108
Sensitivity	0.487
Positive Predictive Value	0.927
Nr of predictions	17

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3GX2_A	SAM links to Rfam database...	0.88	0.79	1.00	22	1427	1	0	0	1	6
3IVN_B	Purine links to Rfam database...	0.71	0.65	0.79	15	884	4	2	2	0	8
3IZ4_A	tmRNA links to Rfam database...	0.46	0.26	0.81	25	25505	8	6	0	2	70
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	2742	0	0	0	0	15
3J3F_8	5_8S_rRNA links to Rfam database...	0.61	0.37	1.00	7	4754	2	0	0	2	12
3LA5_A	Purine links to Rfam database...	0.73	0.64	0.84	16	935	3	1	2	0	9
3NPB_A	SAM links to Rfam database...	0.77	0.59	1.00	22	2256	3	0	0	3	15
3O58_3	5_8S_rRNA links to Rfam database...	0.60	0.36	1.00	8	4756	1	0	0	1	14
3PDR_A	ykoK links to Rfam database...	0.81	0.66	1.00	33	4807	1	0	0	1	17
3RKF_A	Purine links to Rfam database...	0.74	0.67	0.84	16	847	3	1	2	0	8
3SD1_A	THF links to Rfam database...	0.70	0.59	0.85	17	1513	3	2	1	0	12
3ZEX_C	5_8S_rRNA links to Rfam database...	0.49	0.24	1.00	7	5367	2	0	0	2	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.50	0.25	1.00	5	4511	2	0	0	2	15
4AOB_A	SAM links to Rfam database...	0.85	0.72	1.00	21	1416	2	0	0	2	8
4ENB_A	crcB links to Rfam database...	0.63	0.40	1.00	6	466	0	0	0	0	9
4ENC_A	crcB links to Rfam database...	0.63	0.40	1.00	6	490	0	0	0	0	9
4FRG_B	AdoCbl-variant links to Rfam database...	0.84	0.71	1.00	17	1185	0	0	0	0	7

Total Scores
MCC	0.647
Average MCC ± 95% Confidence Intervals	0.652 ± 0.123
Sensitivity	0.569
Positive Predictive Value	0.742
Nr of predictions	17

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3GX2_A	SAM links to Rfam database...	0.88	0.79	1.00	22	1427	1	0	0	1	6
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3IZ4_A	tmRNA links to Rfam database...	0.52	0.41	0.65	39	25476	26	15	6	5	56
3J3E_8	5_8S_rRNA links to Rfam database...	0.19	0.20	0.19	3	2726	21	5	8	8	12
3J3F_8	5_8S_rRNA links to Rfam database...	0.43	0.47	0.39	9	4738	20	6	8	6	10
3LA5_A	Purine links to Rfam database...	0.89	0.80	1.00	20	934	0	0	0	0	5
3NPB_A	SAM links to Rfam database...	0.75	0.57	1.00	21	2257	5	0	0	5	16
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.50	0.52	11	4743	19	5	5	9	11
3PDR_A	ykoK links to Rfam database...	0.84	0.76	0.93	38	4799	5	1	2	2	12
3RKF_A	Purine links to Rfam database...	0.91	0.83	1.00	20	846	0	0	0	0	4
3SD1_A	THF links to Rfam database...	0.81	0.69	0.95	20	1512	1	0	1	0	9
3ZEX_C	5_8S_rRNA links to Rfam database...	0.35	0.31	0.39	9	5351	21	3	11	7	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.25	0.24	5	4495	30	3	13	14	15
4AOB_A	SAM links to Rfam database...	0.70	0.59	0.85	17	1417	4	0	3	1	12
4ENB_A	crcB links to Rfam database...	0.68	0.47	1.00	7	465	0	0	0	0	8
4ENC_A	crcB links to Rfam database...	0.85	0.73	1.00	11	485	0	0	0	0	4
4FRG_B	AdoCbl-variant links to Rfam database...	0.64	0.54	0.76	13	1185	4	0	4	0	11

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