CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASampler(seed)		Vsfold5
MCC	0.663	>	0.632
Average MCC ± 95% Confidence Intervals	0.682 ± 0.128	>	0.674 ± 0.159
Sensitivity	0.515	<	0.571
Positive Predictive Value	0.857	>	0.706
Total TP	252	<	279
Total TN	65818	>	65717
Total FP	60	<	150
Total FP CONTRA	4	<	14
Total FP INCONS	38	<	102
Total FP COMP	18	<	34
Total FN	237	>	210
P-value	2.88234616094e-08

Comparison of performance of RNASampler(seed) and Vsfold5. 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 Vsfold5).
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 Vsfold5).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNASampler(seed) and Vsfold5. 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 Vsfold5).

Total Scores
MCC	0.663
Average MCC ± 95% Confidence Intervals	0.682 ± 0.128
Sensitivity	0.515
Positive Predictive Value	0.857
Nr of predictions	18

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
2KE6_A	K10_TLS links to Rfam database...	0.92	0.84	1.00	16	1112	1	0	0	1	3
2KUR_A	K10_TLS links to Rfam database...	0.90	0.81	1.00	17	1111	0	0	0	0	4
2KUU_A	K10_TLS links to Rfam database...	0.87	0.76	1.00	16	1112	1	0	0	1	5
2KUV_A	K10_TLS links to Rfam database...	0.88	0.77	1.00	17	1111	0	0	0	0	5
2KUW_A	K10_TLS links to Rfam database...	0.90	0.81	1.00	17	1111	0	0	0	0	4
2L1F_A	Gammaretro_CES links to Rfam database...	0.81	0.67	1.00	16	2064	0	0	0	0	8
2L1F_B	Gammaretro_CES links to Rfam database...	0.82	0.68	1.00	17	2128	0	0	0	0	8
2L94_A	HIV_FE links to Rfam database...	0.71	0.55	0.92	11	978	1	0	1	0	9
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1530	10	0	10	0	20
3A3A_A	tRNA-Sec links to Rfam database...	0.70	0.49	1.00	18	3637	0	0	0	0	19
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
3W3S_B	tRNA-Sec links to Rfam database...	0.55	0.30	1.00	12	4741	1	0	0	1	28
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	0.632
Average MCC ± 95% Confidence Intervals	0.674 ± 0.159
Sensitivity	0.571
Positive Predictive Value	0.706
Nr of predictions	18

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...	0.90	0.82	1.00	9	397	0	0	0	0	2
2KE6_A	K10_TLS links to Rfam database...	0.97	0.95	1.00	18	1110	1	0	0	1	1
2KUR_A	K10_TLS links to Rfam database...	0.95	0.90	1.00	19	1109	0	0	0	0	2
2KUU_A	K10_TLS links to Rfam database...	0.92	0.86	1.00	18	1110	1	0	0	1	3
2KUV_A	K10_TLS links to Rfam database...	0.93	0.86	1.00	19	1109	0	0	0	0	3
2KUW_A	K10_TLS links to Rfam database...	0.95	0.90	1.00	19	1109	0	0	0	0	2
2L1F_A	Gammaretro_CES links to Rfam database...	0.69	0.58	0.82	14	2063	3	0	3	0	10
2L1F_B	Gammaretro_CES links to Rfam database...	0.70	0.60	0.83	15	2127	3	0	3	0	10
2L94_A	HIV_FE links to Rfam database...	0.95	0.90	1.00	18	972	0	0	0	0	2
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1527	13	0	13	0	20
3A3A_A	tRNA-Sec links to Rfam database...	0.85	0.73	1.00	27	3628	0	0	0	0	10
3IVN_B	Purine links to Rfam database...	0.76	0.58	1.00	18	2328	0	0	0	0	13
3JYX_4	5_8S_rRNA links to Rfam database...	0.31	0.30	0.31	10	12214	32	3	19	10	23
3O58_3	5_8S_rRNA links to Rfam database...	0.39	0.37	0.41	13	12371	28	7	12	9	22
3RKF_A	Purine links to Rfam database...	0.75	0.65	0.88	22	2186	3	0	3	0	12
3SD1_A	THF links to Rfam database...	0.11	0.10	0.15	4	3890	22	0	22	0	38
3W3S_B	tRNA-Sec links to Rfam database...	0.76	0.70	0.82	28	4719	7	1	5	1	12
4A1C_2	5_8S_rRNA links to Rfam database...	0.24	0.24	0.24	8	11748	37	3	22	12	25

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