CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	Cylofold		Murlet(seed)
MCC	0.579	>	0.479
Average MCC ± 95% Confidence Intervals	0.618 ± 0.149	>	0.484 ± 0.110
Sensitivity	0.492	>	0.287
Positive Predictive Value	0.687	<	0.806
Total TP	257	>	150
Total TN	67864	<	68052
Total FP	139	>	39
Total FP CONTRA	17	>	2
Total FP INCONS	100	>	34
Total FP COMP	22	>	3
Total FN	265	<	372
P-value	2.69132796717e-08

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

Total Scores
MCC	0.579
Average MCC ± 95% Confidence Intervals	0.618 ± 0.149
Sensitivity	0.492
Positive Predictive Value	0.687
Nr of predictions	16

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L1F_B	Gammaretro_CES links to Rfam database...	0.92	0.84	1.00	21	2124	0	0	0	0	4
2L1F_A	Gammaretro_CES links to Rfam database...	0.91	0.83	1.00	20	2060	0	0	0	0	4
2L94_A	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
2LC8_A	GP_knot1 links to Rfam database...	0.61	0.55	0.69	11	1524	5	0	5	0	9
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.38	0.40	0.36	8	4538	23	7	7	9	12
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.10	0.10	0.11	4	5115	32	1	31	0	38
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
3W3S_B	tRNA-Sec links to Rfam database...	0.44	0.38	0.52	15	4724	15	0	14	1	25
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
4FRN_A	AdoCbl-variant links to Rfam database...	0.20	0.14	0.31	5	5135	11	2	9	0	31

Total Scores
MCC	0.479
Average MCC ± 95% Confidence Intervals	0.484 ± 0.110
Sensitivity	0.287
Positive Predictive Value	0.806
Nr of predictions	16

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2L1F_B	Gammaretro_CES links to Rfam database...	0.80	0.72	0.90	18	2125	2	0	2	0	7
2L1F_A	Gammaretro_CES links to Rfam database...	0.82	0.75	0.90	18	2060	2	0	2	0	6
2L94_A	HIV_FE links to Rfam database...	0.59	0.40	0.89	8	981	1	0	1	0	12
2LC8_A	GP_knot1 links to Rfam database...	-0.01	0.00	0.00	0	1528	12	0	12	0	20
2XKV_B	Bacteria_small_SRP links to Rfam database...	0.45	0.20	1.00	4	4556	2	0	0	2	16
2XXA_G	Bacteria_small_SRP links to Rfam database...	0.38	0.14	1.00	6	5145	0	0	0	0	36
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
3W3S_B	tRNA-Sec links to Rfam database...	0.41	0.23	0.75	9	4741	3	0	3	0	31
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
4FRG_B	AdoCbl-variant links to Rfam database...	0.15	0.09	0.25	3	3474	9	0	9	0	29
4FRN_A	AdoCbl-variant links to Rfam database...	0.58	0.39	0.88	14	5135	2	1	1	0	22

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