CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Murlet(20)		Murlet(seed)
MCC	0.567	>	0.496
Average MCC ± 95% Confidence Intervals	0.559 ± 0.099	>	0.499 ± 0.053
Sensitivity	0.405	>	0.277
Positive Predictive Value	0.799	<	0.895
Total TP	199	>	136
Total TN	78789	<	78886
Total FP	64	>	20
Total FP CONTRA	6	>	5
Total FP INCONS	44	>	11
Total FP COMP	14	>	4
Total FN	292	<	355
P-value	2.86595104665e-08

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

Total Scores
MCC	0.567
Average MCC ± 95% Confidence Intervals	0.559 ± 0.099
Sensitivity	0.405
Positive Predictive Value	0.799
Nr of predictions	14

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...	0.67	0.45	1.00	5	401	0	0	0	0	6
3GX2_A	SAM links to Rfam database...	0.61	0.38	1.00	15	4356	1	0	0	1	25
3IVN_B	Purine links to Rfam database...	0.69	0.48	1.00	15	2331	0	0	0	0	16
3JYX_4	5_8S_rRNA links to Rfam database...	0.36	0.27	0.47	9	12227	15	0	10	5	24
3LA5_A	Purine links to Rfam database...	0.68	0.47	1.00	16	2469	0	0	0	0	18
3NPB_A	SAM links to Rfam database...	0.55	0.35	0.89	16	7003	2	1	1	0	30
3O58_3	5_8S_rRNA links to Rfam database...	0.33	0.23	0.47	8	12386	12	2	7	3	27
3PDR_A	ykoK links to Rfam database...	0.70	0.53	0.93	38	12839	3	0	3	0	34
3RKF_A	Purine links to Rfam database...	0.68	0.47	1.00	16	2195	0	0	0	0	18
3SD1_A	THF links to Rfam database...	0.68	0.57	0.83	24	3887	5	1	4	0	18
4A1C_2	5_8S_rRNA links to Rfam database...	0.17	0.15	0.20	5	11756	24	2	18	4	28
4AOB_A	SAM links to Rfam database...	0.72	0.55	0.96	23	4347	2	0	1	1	19
4ENB_A	crcB links to Rfam database...	0.46	0.21	1.00	4	1271	0	0	0	0	15
4ENC_A	crcB links to Rfam database...	0.51	0.26	1.00	5	1321	0	0	0	0	14

Total Scores
MCC	0.496
Average MCC ± 95% Confidence Intervals	0.499 ± 0.053
Sensitivity	0.277
Positive Predictive Value	0.895
Nr of predictions	14

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...	0.52	0.27	1.00	3	403	0	0	0	0	8
3GX2_A	SAM links to Rfam database...	0.59	0.35	1.00	14	4357	1	0	0	1	26
3IVN_B	Purine links to Rfam database...	0.53	0.39	0.75	12	2330	4	2	2	0	19
3JYX_4	5_8S_rRNA links to Rfam database...	0.23	0.09	0.60	3	12241	4	0	2	2	30
3LA5_A	Purine links to Rfam database...	0.58	0.41	0.82	14	2468	3	1	2	0	20
3NPB_A	SAM links to Rfam database...	0.49	0.28	0.87	13	7006	2	1	1	0	33
3O58_3	5_8S_rRNA links to Rfam database...	0.45	0.20	1.00	7	12396	0	0	0	0	28
3PDR_A	ykoK links to Rfam database...	0.44	0.19	1.00	14	12866	0	0	0	0	58
3RKF_A	Purine links to Rfam database...	0.53	0.35	0.80	12	2196	3	1	2	0	22
3SD1_A	THF links to Rfam database...	0.47	0.26	0.85	11	3903	2	0	2	0	31
4A1C_2	5_8S_rRNA links to Rfam database...	0.46	0.21	1.00	7	11774	0	0	0	0	26
4AOB_A	SAM links to Rfam database...	0.58	0.33	1.00	14	4357	1	0	0	1	28
4ENB_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1269	0	0	0	0	13
4ENC_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1320	0	0	0	0	13

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