CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Cylofold		MXScarna(seed)
MCC	0.659	>	0.657
Average MCC ± 95% Confidence Intervals	0.682 ± 0.094	>	0.594 ± 0.144
Sensitivity	0.554	>	0.535
Positive Predictive Value	0.789	<	0.812
Total TP	300	>	290
Total TN	69465	<	69488
Total FP	96	>	87
Total FP CONTRA	12	=	12
Total FP INCONS	68	>	55
Total FP COMP	16	<	20
Total FN	242	<	252
P-value	0.0467887381528

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

Total Scores
MCC	0.659
Average MCC ± 95% Confidence Intervals	0.682 ± 0.094
Sensitivity	0.554
Positive Predictive Value	0.789
Nr of predictions	16

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KX8_A	7SK links to Rfam database...	0.94	0.89	1.00	16	845	0	0	0	0	2
2LC8_A	GP_knot1 links to Rfam database...	0.61	0.55	0.69	11	1524	5	0	5	0	9
2XQD_Y	tRNA links to Rfam database...	0.81	0.78	0.84	21	2825	4	4	0	0	6
3AKZ_H	tRNA links to Rfam database...	0.66	0.57	0.76	16	2680	6	0	5	1	12
3AMU_B	tRNA links to Rfam database...	0.67	0.59	0.76	16	2982	7	0	5	2	11
3IZF_C	5S_rRNA links to Rfam database...	0.68	0.56	0.83	30	6867	6	0	6	0	24
3J16_L	tRNA links to Rfam database...	0.75	0.57	1.00	17	2758	0	0	0	0	13
3O58_3	5_8S_rRNA links to Rfam database...	0.36	0.34	0.38	12	12371	29	5	15	9	23
3O58_2	5S_rRNA links to Rfam database...	0.80	0.68	0.93	26	7232	3	0	2	1	12
3PDR_A	ykoK links to Rfam database...	0.72	0.54	0.95	39	12839	4	0	2	2	33
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...	0.62	0.50	0.78	21	3889	6	0	6	0	21
3UZL_B	tRNA links to Rfam database...	0.45	0.38	0.54	14	3544	12	1	11	0	23
4AOB_A	SAM links to Rfam database...	0.35	0.26	0.48	11	4348	13	1	11	1	31
4ENB_A	crcB links to Rfam database...	0.89	0.79	1.00	15	1260	0	0	0	0	4
4ENC_A	crcB links to Rfam database...	0.86	0.79	0.94	15	1310	1	1	0	0	4

Total Scores
MCC	0.657
Average MCC ± 95% Confidence Intervals	0.594 ± 0.144
Sensitivity	0.535
Positive Predictive Value	0.812
Nr of predictions	16

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KX8_A	7SK links to Rfam database...	-0.01	0.00	0.00	0	859	2	0	2	0	18
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1530	12	0	10	2	20
2XQD_Y	tRNA links to Rfam database...	0.77	0.67	0.90	18	2830	2	0	2	0	9
3AKZ_H	tRNA links to Rfam database...	0.86	0.75	1.00	21	2680	0	0	0	0	7
3AMU_B	tRNA links to Rfam database...	0.84	0.70	1.00	19	2984	1	0	0	1	8
3IZF_C	5S_rRNA links to Rfam database...	0.67	0.57	0.79	31	6864	9	1	7	1	23
3J16_L	tRNA links to Rfam database...	0.82	0.67	1.00	20	2755	0	0	0	0	10
3O58_3	5_8S_rRNA links to Rfam database...	0.45	0.34	0.60	12	12383	19	2	6	11	23
3O58_2	5S_rRNA links to Rfam database...	0.79	0.79	0.79	30	7222	10	4	4	2	8
3PDR_A	ykoK links to Rfam database...	0.73	0.63	0.87	45	12828	9	2	5	2	27
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	1	7	0	19
3UZL_B	tRNA links to Rfam database...	0.66	0.49	0.90	18	3550	2	1	1	0	19
4AOB_A	SAM links to Rfam database...	0.66	0.55	0.79	23	4342	7	0	6	1	19
4ENB_A	crcB links to Rfam database...	0.48	0.32	0.75	6	1267	2	0	2	0	13
4ENC_A	crcB links to Rfam database...	0.43	0.32	0.60	6	1316	4	1	3	0	13

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