CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Pknots		RNASampler(seed)
MCC	0.702	>	0.640
Average MCC ± 95% Confidence Intervals	0.722 ± 0.254	>	0.602 ± 0.309
Sensitivity	0.747	>	0.554
Positive Predictive Value	0.667	<	0.748
Total TP	124	>	92
Total TN	14424	<	14487
Total FP	85	>	44
Total FP CONTRA	30	>	9
Total FP INCONS	32	>	22
Total FP COMP	23	>	13
Total FN	42	<	74
P-value	0.0

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

Total Scores
MCC	0.702
Average MCC ± 95% Confidence Intervals	0.722 ± 0.254
Sensitivity	0.747
Positive Predictive Value	0.667
Nr of predictions	7

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2LC8_A	GP_knot1 links to Rfam database...	0.83	0.83	0.83	15	510	3	2	1	0	3
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	0.87	0.95	20	882	1	0	1	0	3
3O58_3	5_8S_rRNA links to Rfam database...	0.32	0.45	0.24	10	4722	39	18	14	7	12
3RKF_A	Purine links to Rfam database...	0.91	0.88	0.95	21	844	1	0	1	0	3
3SD1_A	THF links to Rfam database...	0.78	0.76	0.81	22	1506	5	1	4	0	7
4A1C_2	5_8S_rRNA links to Rfam database...	0.33	0.40	0.29	8	4488	36	9	11	16	12

Total Scores
MCC	0.640
Average MCC ± 95% Confidence Intervals	0.602 ± 0.309
Sensitivity	0.554
Positive Predictive Value	0.748
Nr of predictions	7

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
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
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.