CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASampler(seed)		RNASampler(20)
MCC	0.541	>	0.528
Average MCC ± 95% Confidence Intervals	0.585 ± 0.177	<	0.589 ± 0.224
Sensitivity	0.399	<	0.426
Positive Predictive Value	0.739	>	0.660
Total TP	116	<	124
Total TN	60338	>	60307
Total FP	60	<	96
Total FP CONTRA	5	<	7
Total FP INCONS	36	<	57
Total FP COMP	19	<	32
Total FN	175	>	167
P-value	0.0

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

Total Scores
MCC	0.541
Average MCC ± 95% Confidence Intervals	0.585 ± 0.177
Sensitivity	0.399
Positive Predictive Value	0.739
Nr of predictions	9

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
2L94_A	HIV_FE links to Rfam database...	0.71	0.55	0.92	11	978	1	0	1	0	9
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
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	0.528
Average MCC ± 95% Confidence Intervals	0.589 ± 0.224
Sensitivity	0.426
Positive Predictive Value	0.660
Nr of predictions	9

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
2L94_A	HIV_FE links to Rfam database...	0.92	0.90	0.95	18	971	1	0	1	0	2
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3JYX_4	5_8S_rRNA links to Rfam database...	0.32	0.30	0.34	10	12217	26	4	15	7	23
3O58_3	5_8S_rRNA links to Rfam database...	0.43	0.34	0.55	12	12381	18	2	8	8	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...	0.67	0.48	0.95	20	3895	1	0	1	0	22
3ZEX_C	5_8S_rRNA links to Rfam database...	0.27	0.19	0.38	10	14170	20	1	15	4	42
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.15	0.23	5	11759	30	0	17	13	28

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