CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASampler(seed)		MXScarna(20)
MCC	0.478	>	0.464
Average MCC ± 95% Confidence Intervals	0.512 ± 0.184	>	0.496 ± 0.190
Sensitivity	0.353	<	0.368
Positive Predictive Value	0.652	>	0.590
Total TP	120	<	125
Total TN	79070	>	79042
Total FP	96	<	148
Total FP CONTRA	8	<	15
Total FP INCONS	56	<	72
Total FP COMP	32	<	61
Total FN	220	>	215
P-value	1.43284180886e-08

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

Total Scores
MCC	0.478
Average MCC ± 95% Confidence Intervals	0.512 ± 0.184
Sensitivity	0.353
Positive Predictive Value	0.652
Nr of predictions	10

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
3IVN_B	Purine links to Rfam database...	0.78	0.61	1.00	19	2327	0	0	0	0	12
3J3E_8	5_8S_rRNA links to Rfam database...	0.12	0.09	0.17	3	7485	22	2	13	7	30
3J3F_8	5_8S_rRNA links to Rfam database...	0.44	0.33	0.57	12	12225	15	1	8	6	24
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	0.464
Average MCC ± 95% Confidence Intervals	0.496 ± 0.190
Sensitivity	0.368
Positive Predictive Value	0.590
Nr of predictions	10

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
3IVN_B	Purine links to Rfam database...	0.74	0.58	0.95	18	2327	1	1	0	0	13
3J3E_8	5_8S_rRNA links to Rfam database...	0.14	0.09	0.23	3	7490	15	2	8	5	30
3J3F_8	5_8S_rRNA links to Rfam database...	0.43	0.36	0.52	13	12221	26	2	10	14	23
3JYX_4	5_8S_rRNA links to Rfam database...	0.33	0.30	0.37	10	12219	32	2	15	15	23
3O58_3	5_8S_rRNA links to Rfam database...	0.52	0.40	0.67	14	12382	17	2	5	10	21
3RKF_A	Purine links to Rfam database...	0.72	0.53	1.00	18	2193	0	0	0	0	16
3SD1_A	THF links to Rfam database...	0.63	0.55	0.74	23	3885	8	2	6	0	19
3ZEX_C	5_8S_rRNA links to Rfam database...	0.31	0.21	0.46	11	14172	13	2	11	0	41
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.15	0.21	5	11757	36	2	17	17	28

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