CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASampler(seed)		Murlet(20)
MCC	0.576	>	0.552
Average MCC ± 95% Confidence Intervals	0.564 ± 0.217	>	0.544 ± 0.201
Sensitivity	0.525	>	0.514
Positive Predictive Value	0.638	>	0.600
Total TP	95	>	93
Total TN	25310	>	25304
Total FP	88	>	84
Total FP CONTRA	21	>	19
Total FP INCONS	33	<	43
Total FP COMP	34	>	22
Total FN	86	<	88
P-value	0.0

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

Total Scores
MCC	0.576
Average MCC ± 95% Confidence Intervals	0.564 ± 0.217
Sensitivity	0.525
Positive Predictive Value	0.638
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3J3E_8	5_8S_rRNA links to Rfam database...	0.18	0.20	0.18	3	2725	22	5	9	8	12
3J3F_8	5_8S_rRNA links to Rfam database...	0.47	0.47	0.47	9	4742	18	5	5	8	10
3O58_3	5_8S_rRNA links to Rfam database...	0.54	0.50	0.58	11	4745	13	5	3	5	11
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...	0.72	0.55	0.94	16	1516	1	0	1	0	13
3ZEX_C	5_8S_rRNA links to Rfam database...	0.39	0.31	0.50	9	5356	14	2	7	5	20
4A1C_2	5_8S_rRNA links to Rfam database...	0.40	0.40	0.40	8	4496	20	4	8	8	12

Total Scores
MCC	0.552
Average MCC ± 95% Confidence Intervals	0.544 ± 0.201
Sensitivity	0.514
Positive Predictive Value	0.600
Nr of predictions	8

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3IVN_B	Purine links to Rfam database...	0.80	0.65	1.00	15	888	0	0	0	0	8
3J3E_8	5_8S_rRNA links to Rfam database...	0.35	0.33	0.38	5	2729	13	2	6	5	10
3J3F_8	5_8S_rRNA links to Rfam database...	0.54	0.53	0.56	10	4743	13	2	6	5	9
3O58_3	5_8S_rRNA links to Rfam database...	0.37	0.32	0.44	7	4748	13	4	5	4	15
3RKF_A	Purine links to Rfam database...	0.81	0.67	1.00	16	850	0	0	0	0	8
3SD1_A	THF links to Rfam database...	0.82	0.83	0.83	24	1504	5	4	1	0	5
3ZEX_C	5_8S_rRNA links to Rfam database...	0.42	0.38	0.48	11	5351	16	2	10	4	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.22	0.25	0.20	5	4491	24	5	15	4	15

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