CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNASampler(seed)		TurboFold(20)
MCC	0.423	>	0.408
Average MCC ± 95% Confidence Intervals	0.424 ± 0.241	>	0.411 ± 0.244
Sensitivity	0.300	<	0.335
Positive Predictive Value	0.600	>	0.503
Total TP	69	<	77
Total TN	51738	>	51700
Total FP	71	<	111
Total FP CONTRA	4	<	7
Total FP INCONS	42	<	69
Total FP COMP	25	<	35
Total FN	161	>	153
P-value	0.0

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

Total Scores
MCC	0.423
Average MCC ± 95% Confidence Intervals	0.424 ± 0.241
Sensitivity	0.300
Positive Predictive Value	0.600
Nr of predictions	6

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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
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	0.408
Average MCC ± 95% Confidence Intervals	0.411 ± 0.244
Sensitivity	0.335
Positive Predictive Value	0.503
Nr of predictions	6

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
3J3E_8	5_8S_rRNA links to Rfam database...	0.17	0.15	0.21	5	7479	28	2	17	9	28
3J3F_8	5_8S_rRNA links to Rfam database...	0.38	0.36	0.39	13	12213	34	2	18	14	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...	0.59	0.48	0.74	20	3889	7	1	6	0	22
3ZEX_C	5_8S_rRNA links to Rfam database...	0.39	0.27	0.56	14	14171	14	2	9	3	38
4A1C_2	5_8S_rRNA links to Rfam database...	0.18	0.15	0.21	5	11757	28	0	19	9	28

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