CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASampler(seed)		RSpredict(20)
MCC	0.478	>	0.415
Average MCC ± 95% Confidence Intervals	0.512 ± 0.184	>	0.451 ± 0.211
Sensitivity	0.353	<	0.362
Positive Predictive Value	0.652	>	0.480
Total TP	120	<	123
Total TN	79070	>	78998
Total FP	96	<	160
Total FP CONTRA	8	<	32
Total FP INCONS	56	<	101
Total FP COMP	32	>	27
Total FN	220	>	217
P-value	8.61680779366e-09

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

Total Scores
MCC	0.478
Average MCC ± 95% Confidence Intervals	0.512 ± 0.184
Sensitivity	0.353
Positive Predictive Value	0.652
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3J3E_8	5_8S_rRNA links to Rfam database...	0.12	0.09	0.17	3	7485	22	2	13	7	30
3J3F_8	5_8S_rRNA links to Rfam database...	0.44	0.33	0.57	12	12225	15	1	8	6	24
3JYX_4	5_8S_rRNA links to Rfam database...	0.39	0.30	0.50	10	12226	13	2	8	3	23
3O58_3	5_8S_rRNA links to Rfam database...	0.45	0.34	0.60	12	12383	12	2	6	4	23
3RKF_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2191	0	0	0	0	14
3SD1_A	THF links to Rfam database...	0.60	0.38	0.94	16	3899	1	0	1	0	26
3ZEX_C	5_8S_rRNA links to Rfam database...	0.32	0.19	0.53	10	14177	13	1	8	4	42
4A1C_2	5_8S_rRNA links to Rfam database...	0.31	0.24	0.40	8	11761	20	0	12	8	25

Total Scores
MCC	0.415
Average MCC ± 95% Confidence Intervals	0.451 ± 0.211
Sensitivity	0.362
Positive Predictive Value	0.480
Nr of predictions	10

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.85	0.73	1.00	8	398	0	0	0	0	3
3IVN_B	Purine links to Rfam database...	0.78	0.65	0.95	20	2325	1	0	1	0	11
3J3E_8	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7484	19	4	15	0	33
3J3F_8	5_8S_rRNA links to Rfam database...	0.39	0.33	0.46	12	12220	23	2	12	9	24
3JYX_4	5_8S_rRNA links to Rfam database...	0.28	0.27	0.30	9	12216	33	5	16	12	24
3O58_3	5_8S_rRNA links to Rfam database...	0.32	0.34	0.30	12	12363	28	12	16	0	23
3RKF_A	Purine links to Rfam database...	0.77	0.62	0.95	21	2189	1	0	1	0	13
3SD1_A	THF links to Rfam database...	0.68	0.60	0.78	25	3884	7	1	6	0	17
3ZEX_C	5_8S_rRNA links to Rfam database...	0.26	0.19	0.36	10	14168	18	2	16	0	42
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.18	0.20	6	11751	30	6	18	6	27

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