CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	CentroidFold		RNASampler(seed)
MCC	0.707	>	0.665
Average MCC ± 95% Confidence Intervals	0.741 ± 0.151	>	0.674 ± 0.140
Sensitivity	0.626	>	0.525
Positive Predictive Value	0.804	<	0.846
Total TP	274	>	230
Total TN	60612	<	60681
Total FP	78	>	59
Total FP CONTRA	12	>	4
Total FP INCONS	55	>	38
Total FP COMP	11	<	17
Total FN	164	<	208
P-value	2.26346675981e-08

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

Total Scores
MCC	0.707
Average MCC ± 95% Confidence Intervals	0.741 ± 0.151
Sensitivity	0.626
Positive Predictive Value	0.804
Nr of predictions	16

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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_B	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	24	2121	0	0	0	0	1
2L1F_A	Gammaretro_CES links to Rfam database...	0.98	0.96	1.00	23	2057	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
2LC8_A	GP_knot1 links to Rfam database...	0.49	0.35	0.70	7	1530	3	1	2	0	13
3A3A_A	tRNA-Sec links to Rfam database...	0.87	0.76	1.00	28	3627	0	0	0	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...	0.23	0.21	0.25	7	12218	25	5	16	4	26
3O58_3	5_8S_rRNA links to Rfam database...	0.38	0.29	0.50	10	12383	10	0	10	0	25
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...	0.58	0.48	0.71	20	3888	8	1	7	0	22
4A1C_2	5_8S_rRNA links to Rfam database...	0.16	0.15	0.17	5	11752	29	5	19	5	28

Total Scores
MCC	0.665
Average MCC ± 95% Confidence Intervals	0.674 ± 0.140
Sensitivity	0.525
Positive Predictive Value	0.846
Nr of predictions	16

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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_B	Gammaretro_CES links to Rfam database...	0.82	0.68	1.00	17	2128	0	0	0	0	8
2L1F_A	Gammaretro_CES links to Rfam database...	0.81	0.67	1.00	16	2064	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
4A1C_2	5_8S_rRNA links to Rfam database...	0.31	0.24	0.40	8	11761	20	0	12	8	25

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