CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Cylofold		Multilign(20)
MCC	0.691	>	0.666
Average MCC ± 95% Confidence Intervals	0.742 ± 0.154	>	0.654 ± 0.189
Sensitivity	0.682	>	0.619
Positive Predictive Value	0.711	<	0.727
Total TP	217	>	197
Total TN	17407	<	17441
Total FP	99	>	92
Total FP CONTRA	18	>	14
Total FP INCONS	70	>	60
Total FP COMP	11	<	18
Total FN	101	<	121
P-value	7.39512130982e-06

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

Total Scores
MCC	0.691
Average MCC ± 95% Confidence Intervals	0.742 ± 0.154
Sensitivity	0.682
Positive Predictive Value	0.711
Nr of predictions	13

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.10	0.11	0.11	4	2009	32	2	30	0	31
3AMU_B	tRNA links to Rfam database...	0.77	0.79	0.75	15	1137	8	0	5	3	4
3J20_0	tRNA links to Rfam database...	0.74	0.76	0.73	16	1197	7	3	3	1	5
3J20_1	tRNA links to Rfam database...	0.71	0.75	0.68	15	1090	8	2	5	1	5
3J2L_3	5S_rRNA links to Rfam database...	0.71	0.68	0.74	23	2989	11	0	8	3	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...	0.71	0.69	0.74	20	1506	7	2	5	0	9
3ZEX_D	5S_rRNA links to Rfam database...	0.69	0.69	0.71	24	2762	11	5	5	1	11
4AOB_A	SAM links to Rfam database...	0.42	0.38	0.48	11	1414	13	3	9	1	18
4ENB_A	crcB links to Rfam database...	1.00	1.00	1.00	15	457	0	0	0	0	0
4ENC_A	crcB links to Rfam database...	0.97	1.00	0.94	15	480	1	1	0	0	0
4FRG_B	AdoCbl-variant links to Rfam database...	0.93	0.88	1.00	21	1181	0	0	0	0	3

Total Scores
MCC	0.666
Average MCC ± 95% Confidence Intervals	0.654 ± 0.189
Sensitivity	0.619
Positive Predictive Value	0.727
Nr of predictions	13

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L94_A	HIV_FE links to Rfam database...	1.00	1.00	1.00	18	339	1	0	0	1	0
2XXA_G	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	2033	12	2	10	0	35
3AMU_B	tRNA links to Rfam database...	0.71	0.74	0.70	14	1137	9	0	6	3	5
3J20_0	tRNA links to Rfam database...	0.68	0.71	0.65	15	1196	9	2	6	1	6
3J20_1	tRNA links to Rfam database...	1.00	1.00	1.00	20	1092	1	0	0	1	0
3J2L_3	5S_rRNA links to Rfam database...	0.80	0.79	0.82	27	2987	10	0	6	4	7
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...	0.68	0.69	0.69	20	1504	9	4	5	0	9
3ZEX_D	5S_rRNA links to Rfam database...	0.88	0.83	0.94	29	2765	8	0	2	6	6
4AOB_A	SAM links to Rfam database...	0.59	0.55	0.64	16	1412	10	3	6	1	13
4ENB_A	crcB links to Rfam database...	0.39	0.33	0.50	5	462	6	0	5	1	10
4ENC_A	crcB links to Rfam database...	0.73	0.60	0.90	9	486	1	1	0	0	6
4FRG_B	AdoCbl-variant links to Rfam database...	0.13	0.13	0.17	3	1184	15	2	13	0	21

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