CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	McQFold		RNASampler(seed)
MCC	0.776	>	0.765
Average MCC ± 95% Confidence Intervals	0.805 ± 0.136	>	0.764 ± 0.134
Sensitivity	0.797	>	0.687
Positive Predictive Value	0.762	<	0.859
Total TP	275	>	237
Total TN	23380	<	23465
Total FP	106	>	62
Total FP CONTRA	45	>	15
Total FP INCONS	41	>	24
Total FP COMP	20	<	23
Total FN	70	<	108
P-value	4.80024504584e-05

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

Total Scores
MCC	0.776
Average MCC ± 95% Confidence Intervals	0.805 ± 0.136
Sensitivity	0.797
Positive Predictive Value	0.762
Nr of predictions	17

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...	1.00	1.00	1.00	10	164	0	0	0	0	0
2KE6_A	K10_TLS links to Rfam database...	0.91	0.83	1.00	15	452	1	0	0	1	3
2KUR_A	K10_TLS links to Rfam database...	0.91	0.84	1.00	16	451	0	0	0	0	3
2KUU_A	K10_TLS links to Rfam database...	0.91	0.83	1.00	15	432	1	0	0	1	3
2KUV_A	K10_TLS links to Rfam database...	0.91	0.84	1.00	16	423	0	0	0	0	3
2KUW_A	K10_TLS links to Rfam database...	0.94	0.89	1.00	16	454	0	0	0	0	2
2L1F_A	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	23	740	0	0	0	0	0
2L1F_B	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	24	767	0	0	0	0	0
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2LC8_A	GP_knot1 links to Rfam database...	0.64	0.61	0.69	11	512	5	1	4	0	7
3A3A_A	tRNA-Sec links to Rfam database...	0.97	0.93	1.00	28	1472	0	0	0	0	2
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3JYX_4	5_8S_rRNA links to Rfam database...	0.35	0.58	0.22	7	4724	33	17	8	8	5
3O58_3	5_8S_rRNA links to Rfam database...	0.30	0.36	0.25	8	4732	27	15	9	3	14
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...	0.82	0.83	0.83	24	1504	5	1	4	0	5
4A1C_2	5_8S_rRNA links to Rfam database...	0.19	0.25	0.16	5	4484	33	11	16	6	15

Total Scores
MCC	0.765
Average MCC ± 95% Confidence Intervals	0.764 ± 0.134
Sensitivity	0.687
Positive Predictive Value	0.859
Nr of predictions	17

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...	1.00	1.00	1.00	10	164	0	0	0	0	0
2KE6_A	K10_TLS links to Rfam database...	0.94	0.89	1.00	16	451	1	0	0	1	2
2KUR_A	K10_TLS links to Rfam database...	0.94	0.89	1.00	17	450	0	0	0	0	2
2KUU_A	K10_TLS links to Rfam database...	0.94	0.89	1.00	16	431	1	0	0	1	2
2KUV_A	K10_TLS links to Rfam database...	0.94	0.89	1.00	17	422	0	0	0	0	2
2KUW_A	K10_TLS links to Rfam database...	0.94	0.89	1.00	16	454	1	0	0	1	2
2L1F_A	Gammaretro_CES links to Rfam database...	0.83	0.70	1.00	16	747	0	0	0	0	7
2L1F_B	Gammaretro_CES links to Rfam database...	0.84	0.71	1.00	17	774	0	0	0	0	7
2L94_A	HIV_FE links to Rfam database...	0.70	0.56	0.91	10	346	2	0	1	1	8
2LC8_A	GP_knot1 links to Rfam database...	-0.03	0.00	0.00	0	518	10	0	10	0	18
3A3A_A	tRNA-Sec links to Rfam database...	0.77	0.60	1.00	18	1482	0	0	0	0	12
3IVN_B	Purine links to Rfam database...	0.91	0.83	1.00	19	884	0	0	0	0	4
3JYX_4	5_8S_rRNA links to Rfam database...	0.70	0.83	0.59	10	4739	13	6	1	6	2
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
4A1C_2	5_8S_rRNA links to Rfam database...	0.40	0.40	0.40	8	4496	20	4	8	8	12

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