CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Cylofold		Carnac(20)
MCC	0.642	>	0.619
Average MCC ± 95% Confidence Intervals	0.658 ± 0.086	>	0.564 ± 0.129
Sensitivity	0.543	>	0.436
Positive Predictive Value	0.765	<	0.882
Total TP	336	>	270
Total TN	85120	<	85253
Total FP	123	>	47
Total FP CONTRA	16	>	1
Total FP INCONS	87	>	35
Total FP COMP	20	>	11
Total FN	283	<	349
P-value	2.76499031155e-08

Comparison of performance of Cylofold and Carnac(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 Cylofold and Carnac(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 Cylofold and Carnac(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for Cylofold and Carnac(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 Cylofold and Carnac(20)).

Total Scores
MCC	0.642
Average MCC ± 95% Confidence Intervals	0.658 ± 0.086
Sensitivity	0.543
Positive Predictive Value	0.765
Nr of predictions	17

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2XQD_Y	tRNA links to Rfam database...	0.81	0.78	0.84	21	2825	4	4	0	0	6
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
3J20_1	tRNA links to Rfam database...	0.69	0.70	0.70	16	2903	7	2	5	0	7
3J20_0	tRNA links to Rfam database...	0.66	0.57	0.77	17	2828	6	1	4	1	13
3J2L_3	5S_rRNA links to Rfam database...	0.56	0.43	0.72	23	7843	11	0	9	2	30
3O58_2	5S_rRNA links to Rfam database...	0.80	0.68	0.93	26	7232	3	0	2	1	12
3O58_3	5_8S_rRNA links to Rfam database...	0.36	0.34	0.38	12	12371	29	5	15	9	23
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
3ZEX_D	5S_rRNA links to Rfam database...	0.58	0.49	0.69	24	6986	11	0	11	0	25
3ZND_W	tRNA links to Rfam database...	0.40	0.39	0.41	9	2981	15	2	11	2	14
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
4FRG_B	AdoCbl-variant links to Rfam database...	0.81	0.66	1.00	21	3465	0	0	0	0	11

Total Scores
MCC	0.619
Average MCC ± 95% Confidence Intervals	0.564 ± 0.129
Sensitivity	0.436
Positive Predictive Value	0.882
Nr of predictions	17

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2XQD_Y	tRNA links to Rfam database...	0.79	0.63	1.00	17	2833	0	0	0	0	10
3AMU_B	tRNA links to Rfam database...	0.69	0.59	0.80	16	2983	6	0	4	2	11
3IZF_C	5S_rRNA links to Rfam database...	0.73	0.56	0.97	30	6872	1	0	1	0	24
3J20_1	tRNA links to Rfam database...	0.86	0.74	1.00	17	2909	0	0	0	0	6
3J20_0	tRNA links to Rfam database...	0.62	0.53	0.73	16	2828	7	0	6	1	14
3J2L_3	5S_rRNA links to Rfam database...	0.46	0.34	0.64	18	7847	11	0	10	1	35
3O58_2	5S_rRNA links to Rfam database...	0.83	0.71	0.96	27	7232	2	0	1	1	11
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.26	1.00	9	12394	0	0	0	0	26
3PDR_A	ykoK links to Rfam database...	0.62	0.40	0.97	29	12850	3	0	1	2	43
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_D	5S_rRNA links to Rfam database...	0.73	0.53	1.00	26	6995	0	0	0	0	23
3ZND_W	tRNA links to Rfam database...	0.47	0.39	0.56	9	2987	10	0	7	3	14
4AOB_A	SAM links to Rfam database...	0.49	0.33	0.74	14	4352	6	1	4	1	28
4ENB_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1275	0	0	0	0	19
4ENC_A	crcB links to Rfam database...	0.00	0.00	0.00	0	1326	0	0	0	0	19
4FRG_B	AdoCbl-variant links to Rfam database...	0.43	0.19	1.00	6	3480	0	0	0	0	26

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