CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	CentroidAlifold(seed)		RNASampler(20)
MCC	0.792	>	0.590
Average MCC ± 95% Confidence Intervals	0.810 ± 0.023	>	0.575 ± 0.041
Sensitivity	0.674	>	0.389
Positive Predictive Value	0.931	>	0.898
Total TP	4770	>	2750
Total TN	2341630	<	2343690
Total FP	811	>	493
Total FP CONTRA	46	>	38
Total FP INCONS	306	>	274
Total FP COMP	459	>	181
Total FN	2305	<	4325
P-value	3.56938820447e-08

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Performance plots

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

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Performance of CentroidAlifold(seed) - scored higher in this pairwise comparison

1. Total counts & total scores for CentroidAlifold(seed)

Total Base Pair Counts
Total TP	4770
Total TN	2341630
Total FP	811
Total FP CONTRA	46
Total FP INCONS	306
Total FP COMP	459
Total FN	2305

Total Scores
MCC	0.792
Average MCC ± 95% Confidence Intervals	0.810 ± 0.023
Sensitivity	0.674
Positive Predictive Value	0.931
Nr of predictions	178

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2. Individual counts for CentroidAlifold(seed) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
ASE_00064	RNaseP_bact_a links to Rfam database...	0.77	0.60	1.00	53	45398	0	0	0	0	36
ASE_00090	RNaseP_bact_a links to Rfam database...	0.75	0.56	1.00	57	55554	0	0	0	0	44
ASE_00135	RNaseP_bact_a links to Rfam database...	0.53	0.39	0.74	42	63133	15	0	15	0	67
ASE_00153	RNaseP_nuc links to Rfam database...	0.67	0.53	0.85	39	57584	7	1	6	0	34
ASE_00215	RNaseP_bact_a links to Rfam database...	0.51	0.32	0.82	32	48477	7	0	7	0	67
ASE_00305	RNaseP_bact_b links to Rfam database...	0.87	0.79	0.96	67	54545	8	0	3	5	18
ASE_00328	RNaseP_bact_b links to Rfam database...	0.83	0.70	1.00	78	72693	5	0	0	5	34
ASE_00361	RNaseP_bact_a links to Rfam database...	0.65	0.43	0.98	55	75410	1	1	0	0	72
ASE_00427	RNaseP_nuc links to Rfam database...	0.86	0.74	1.00	34	40721	0	0	0	0	12
ASE_00441	RNaseP_bact_a links to Rfam database...	0.65	0.44	0.96	49	64210	3	0	2	1	63
PDB_00012	mir-TAR links to Rfam database...	1.00	1.00	1.00	7	399	2	0	0	2	0
PDB_00213	Gammaretro_CES links to Rfam database...	0.85	0.73	1.00	30	5020	0	0	0	0	11
PDB_00553	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	455	0	0	0	0	1
PDB_00741	Entero_5_CRE links to Rfam database...	0.72	0.53	1.00	9	694	0	0	0	0	8
PDB_00810	s2m links to Rfam database...	0.87	0.76	1.00	13	1068	1	0	0	1	4
PDB_00828	Purine links to Rfam database...	0.88	0.78	1.00	21	2464	0	0	0	0	6
PDB_00829	Purine links to Rfam database...	0.91	0.83	1.00	20	2258	0	0	0	0	4
PDB_00876	HIV_FE links to Rfam database...	0.53	0.50	0.59	10	973	7	0	7	0	10
PDB_01020	Purine links to Rfam database...	0.91	0.83	1.00	19	2259	1	0	0	1	4
PDB_01050	UnaL2 links to Rfam database...	0.68	0.46	1.00	6	624	2	0	0	2	7
PDB_01073	SAM links to Rfam database...	0.84	0.71	1.00	24	4347	1	0	0	1	10
PDB_01114	TPP links to Rfam database...	0.77	0.59	1.00	16	2834	1	0	0	1	11
PDB_01152	HIV_FS2 links to Rfam database...	0.80	0.64	1.00	9	552	0	0	0	0	5
PDB_01236	ykoK links to Rfam database...	0.88	0.78	1.00	42	11586	3	0	0	3	12
RFA_00389	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	3	0	0	3	1
RFA_00390	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	2	0	0	2	1
RFA_00391	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	3	0	0	3	1
RFA_00396	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	3	0	0	3	1
RFA_00402	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	3	0	0	3	1
RFA_00409	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	3	0	0	3	1
RFA_00416	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1471	2	0	0	2	1
RFA_00433	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	2	0	0	2	1
RFA_00434	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	3	0	0	3	1
RFA_00436	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	3	0	0	3	1
RFA_00440	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1471	3	0	0	3	1
RFA_00442	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	3	0	0	3	1
RFA_00444	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1526	3	0	0	3	1
RFA_00583	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4935	3	0	0	3	0
RFA_00584	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	2911	3	0	0	3	0
RFA_00585	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	3	0	0	3	0
RFA_00586	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	3901	3	0	0	3	0
RFA_00587	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	3	0	0	3	0
RFA_00588	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4545	3	0	0	3	0
RFA_00589	Y_RNA links to Rfam database...	0.97	0.93	1.00	14	4357	3	0	0	3	1
RFA_00594	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	2760	3	0	0	3	0
RFA_00596	Y_RNA links to Rfam database...	0.93	0.87	1.00	13	5982	3	0	0	3	2
RFA_00658	Hammerhead_1 links to Rfam database...	0.71	0.57	0.89	8	1119	2	0	1	1	6
RFA_00664	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	984	0	0	0	0	8
RFA_00667	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	984	0	0	0	0	8
RFA_00668	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	984	0	0	0	0	8
RFA_00672	Hammerhead_1 links to Rfam database...	0.78	0.62	1.00	8	895	0	0	0	0	5
RFA_00673	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	1122	0	0	0	0	8
RFA_00674	Hammerhead_1 links to Rfam database...	0.60	0.43	0.86	6	1121	1	0	1	0	8
RFA_00675	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	984	0	0	0	0	8
RFA_00677	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	984	0	0	0	0	8
RFA_00678	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	940	0	0	0	0	8
RFA_00680	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	1122	0	0	0	0	8
RFA_00704	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	984	0	0	0	0	8
RFA_00707	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	1029	0	0	0	0	8
RFA_00715	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	940	0	0	0	0	8
RFA_00717	Hammerhead_1 links to Rfam database...	0.75	0.57	1.00	8	895	0	0	0	0	6
RFA_00730	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00731	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00733	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00734	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00736	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00737	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00745	s2m links to Rfam database...	1.00	1.00	1.00	12	934	2	0	0	2	0
RFA_00749	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00758	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00762	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00763	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00764	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00765	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00786	Gammaretro_CES links to Rfam database...	0.97	0.94	1.00	30	5020	0	0	0	0	2
RFA_00791	Gammaretro_CES links to Rfam database...	0.97	0.94	1.00	30	5121	0	0	0	0	2
RFA_00792	Gammaretro_CES links to Rfam database...	0.97	0.94	1.00	30	5020	0	0	0	0	2
RFA_00801	Gammaretro_CES links to Rfam database...	0.97	0.94	1.00	30	5020	0	0	0	0	2
SPR_00273	tRNA links to Rfam database...	0.44	0.24	0.83	5	2844	1	0	1	0	16
SPR_00277	tRNA links to Rfam database...	0.53	0.29	1.00	6	2920	0	0	0	0	15
SPR_00721	tRNA links to Rfam database...	0.53	0.29	1.00	6	2920	0	0	0	0	15
SPR_01157	tRNA links to Rfam database...	0.53	0.29	1.00	6	2769	0	0	0	0	15
SRP_00006	Metazoa_SRP links to Rfam database...	0.91	0.82	1.00	83	45670	7	0	0	7	18
SRP_00008	Bacteria_small_SRP links to Rfam database...	0.96	0.92	1.00	23	2903	2	0	0	2	2
SRP_00011	Plant_SRP links to Rfam database...	0.81	0.74	0.89	77	46273	15	0	10	5	27
SRP_00015	Plant_SRP links to Rfam database...	0.82	0.75	0.89	74	46277	19	0	9	10	25
SRP_00020	Bacteria_small_SRP links to Rfam database...	0.89	0.85	0.93	28	5535	2	1	1	0	5
SRP_00024	Bacteria_large_SRP links to Rfam database...	0.56	0.31	1.00	27	37648	4	0	0	4	60
SRP_00026	Bacteria_large_SRP links to Rfam database...	0.55	0.31	1.00	27	36829	4	0	0	4	61
SRP_00030	Bacteria_large_SRP links to Rfam database...	0.55	0.31	1.00	27	36829	4	0	0	4	61
SRP_00031	Bacteria_large_SRP links to Rfam database...	0.54	0.29	1.00	26	36289	5	0	0	5	63
SRP_00037	Bacteria_large_SRP links to Rfam database...	0.56	0.31	1.00	27	36558	4	0	0	4	60
SRP_00038	Bacteria_small_SRP links to Rfam database...	0.90	0.82	1.00	27	5023	3	0	0	3	6
SRP_00042	Bacteria_small_SRP links to Rfam database...	0.85	0.80	0.91	20	3983	6	1	1	4	5
SRP_00044	Bacteria_small_SRP links to Rfam database...	0.85	0.81	0.90	26	6076	4	1	2	1	6
SRP_00046	Bacteria_small_SRP links to Rfam database...	0.94	0.88	1.00	28	4725	2	0	0	2	4
SRP_00050	Metazoa_SRP links to Rfam database...	0.94	0.88	1.00	87	44763	5	0	0	5	12
SRP_00051	Bacteria_small_SRP links to Rfam database...	0.76	0.67	0.87	20	5437	7	0	3	4	10
SRP_00054	Bacteria_small_SRP links to Rfam database...	0.92	0.84	1.00	27	5538	3	0	0	3	5
SRP_00057	Bacteria_small_SRP links to Rfam database...	0.79	0.69	0.92	24	6302	6	1	1	4	11
SRP_00058	Bacteria_small_SRP links to Rfam database...	0.88	0.82	0.93	28	5748	2	1	1	0	6
SRP_00066	Metazoa_SRP links to Rfam database...	0.91	0.82	1.00	82	45369	10	0	0	10	18
SRP_00074	Bacteria_small_SRP links to Rfam database...	0.52	0.48	0.56	14	6530	16	0	11	5	15
SRP_00075	Bacteria_small_SRP links to Rfam database...	0.34	0.32	0.37	11	5535	19	0	19	0	23
SRP_00077	Bacteria_small_SRP links to Rfam database...	0.59	0.51	0.68	19	6642	11	0	9	2	18
SRP_00084	Bacteria_small_SRP links to Rfam database...	0.88	0.82	0.93	28	5430	2	1	1	0	6
SRP_00086	Metazoa_SRP links to Rfam database...	0.94	0.88	1.00	88	44165	4	0	0	4	12
SRP_00088	Bacteria_large_SRP links to Rfam database...	0.55	0.30	1.00	27	34164	4	0	0	4	62
SRP_00089	Bacteria_large_SRP links to Rfam database...	0.55	0.30	1.00	27	35751	4	0	0	4	63
SRP_00090	Bacteria_large_SRP links to Rfam database...	0.55	0.30	1.00	27	35484	4	0	0	4	63
SRP_00094	Bacteria_small_SRP links to Rfam database...	0.82	0.83	0.80	20	4070	9	1	4	4	4
SRP_00095	Bacteria_small_SRP links to Rfam database...	0.82	0.84	0.81	21	3979	8	1	4	3	4
SRP_00098	Bacteria_small_SRP links to Rfam database...	0.65	0.57	0.75	21	6413	9	1	6	2	16
SRP_00102	Metazoa_SRP links to Rfam database...	0.93	0.86	1.00	87	44464	5	0	0	5	14
SRP_00103	Metazoa_SRP links to Rfam database...	0.93	0.86	1.00	88	45363	4	0	0	4	14
SRP_00105	Bacteria_small_SRP links to Rfam database...	0.89	0.79	1.00	27	5538	3	0	0	3	7
SRP_00107	Bacteria_small_SRP links to Rfam database...	0.46	0.53	0.40	10	3630	19	3	12	4	9
SRP_00121	Bacteria_small_SRP links to Rfam database...	0.82	0.80	0.83	20	4254	6	0	4	2	5
SRP_00128	Bacteria_small_SRP links to Rfam database...	0.82	0.72	0.93	26	6758	4	1	1	2	10
SRP_00132	Bacteria_small_SRP links to Rfam database...	0.73	0.69	0.77	20	4825	9	0	6	3	9
SRP_00134	Bacteria_large_SRP links to Rfam database...	0.70	0.62	0.78	18	5972	13	0	5	8	11
SRP_00141	Bacteria_small_SRP links to Rfam database...	0.78	0.66	0.93	27	6299	3	1	1	1	14
SRP_00152	Plant_SRP links to Rfam database...	0.86	0.79	0.93	81	45666	11	0	6	5	22
SRP_00161	Bacteria_small_SRP links to Rfam database...	0.84	0.82	0.86	18	2829	5	0	3	2	4
SRP_00162	Bacteria_small_SRP links to Rfam database...	0.87	0.87	0.87	20	2903	4	0	3	1	3
SRP_00163	Bacteria_small_SRP links to Rfam database...	0.84	0.81	0.88	21	3462	5	0	3	2	5
SRP_00164	Bacteria_small_SRP links to Rfam database...	0.78	0.66	0.92	23	6878	7	1	1	5	12
SRP_00170	Bacteria_small_SRP links to Rfam database...	0.83	0.76	0.90	19	4074	6	1	1	4	6
SRP_00171	Metazoa_SRP links to Rfam database...	0.92	0.85	1.00	75	45376	17	0	0	17	13
SRP_00178	Plant_SRP links to Rfam database...	0.91	0.83	0.99	85	45667	7	0	1	6	17
SRP_00179	Plant_SRP links to Rfam database...	0.89	0.79	1.00	83	45973	9	0	0	9	22
SRP_00181	Plant_SRP links to Rfam database...	0.85	0.78	0.93	80	45970	13	0	6	7	22
SRP_00182	Plant_SRP links to Rfam database...	0.87	0.79	0.95	80	45972	11	0	4	7	21
SRP_00188	Plant_SRP links to Rfam database...	0.88	0.85	0.91	67	31051	13	0	7	6	12
SRP_00194	Bacteria_small_SRP links to Rfam database...	0.71	0.71	0.71	15	3219	9	0	6	3	6
SRP_00200	Bacteria_small_SRP links to Rfam database...	0.77	0.67	0.89	24	6876	6	1	2	3	12
SRP_00209	Bacteria_small_SRP links to Rfam database...	0.75	0.74	0.77	20	4630	9	1	5	3	7
SRP_00213	Bacteria_small_SRP links to Rfam database...	0.92	0.92	0.92	23	4161	6	1	1	4	2
SRP_00215	Bacteria_small_SRP links to Rfam database...	0.86	0.84	0.88	21	3216	4	0	3	1	4
SRP_00227	Bacteria_small_SRP links to Rfam database...	0.86	0.81	0.93	25	5124	5	1	1	3	6
SRP_00228	Metazoa_SRP links to Rfam database...	0.92	0.86	0.99	82	45368	10	0	1	9	13
SRP_00231	Bacteria_small_SRP links to Rfam database...	0.88	0.82	0.93	28	5430	2	1	1	0	6
SRP_00233	Bacteria_small_SRP links to Rfam database...	0.87	0.82	0.93	27	5122	3	0	2	1	6
SRP_00234	Bacteria_large_SRP links to Rfam database...	0.55	0.30	1.00	26	36289	5	0	0	5	60
SRP_00243	Bacteria_small_SRP links to Rfam database...	0.88	0.81	0.96	25	5125	5	0	1	4	6
SRP_00244	Bacteria_small_SRP links to Rfam database...	0.74	0.62	0.89	24	6876	5	1	2	2	15
SRP_00250	Bacteria_small_SRP links to Rfam database...	0.67	0.58	0.78	21	6759	9	1	5	3	15
SRP_00251	Bacteria_small_SRP links to Rfam database...	0.77	0.67	0.89	24	6994	6	1	2	3	12
SRP_00266	Bacteria_small_SRP links to Rfam database...	0.55	0.55	0.55	16	4627	14	2	11	1	13
SRP_00268	Bacteria_small_SRP links to Rfam database...	0.91	0.89	0.92	24	4160	5	1	1	3	3
SRP_00269	Bacteria_small_SRP links to Rfam database...	0.68	0.64	0.72	21	5021	9	0	8	1	12
SRP_00270	Bacteria_small_SRP links to Rfam database...	0.86	0.81	0.93	25	4629	5	0	2	3	6
SRP_00271	Bacteria_small_SRP links to Rfam database...	0.89	0.88	0.91	21	3217	3	0	2	1	3
SRP_00273	Bacteria_small_SRP links to Rfam database...	0.79	0.68	0.93	27	6757	3	1	1	1	13
SRP_00274	Bacteria_small_SRP links to Rfam database...	0.81	0.71	0.93	27	6874	3	1	1	1	11
SRP_00295	Bacteria_small_SRP links to Rfam database...	0.78	0.66	0.93	25	6876	5	1	1	3	13
SRP_00303	Bacteria_small_SRP links to Rfam database...	0.68	0.63	0.74	20	6643	10	1	6	3	12
SRP_00308	Bacteria_large_SRP links to Rfam database...	0.55	0.31	1.00	27	36288	4	0	0	4	61
SRP_00312	Bacteria_small_SRP links to Rfam database...	0.91	0.89	0.92	24	4160	5	1	1	3	3
SRP_00315	Bacteria_small_SRP links to Rfam database...	0.81	0.83	0.79	19	2902	5	0	5	0	4
SRP_00317	Metazoa_SRP links to Rfam database...	0.90	0.84	0.98	82	45066	10	0	2	8	16
SRP_00318	Bacteria_small_SRP links to Rfam database...	0.81	0.83	0.79	19	2979	5	0	5	0	4
SRP_00325	Bacteria_small_SRP links to Rfam database...	0.87	0.82	0.93	27	4342	3	0	2	1	6
SRP_00326	Bacteria_small_SRP links to Rfam database...	0.86	0.81	0.93	25	5023	5	0	2	3	6
SRP_00333	Bacteria_small_SRP links to Rfam database...	0.86	0.79	0.93	27	5122	3	0	2	1	7
SRP_00335	Bacteria_large_SRP links to Rfam database...	0.46	0.38	0.56	15	35218	16	7	5	4	24
SRP_00337	Bacteria_large_SRP links to Rfam database...	0.54	0.30	1.00	27	35484	4	0	0	4	64
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.90	0.81	1.00	29	5431	1	0	0	1	7
SRP_00341	Bacteria_small_SRP links to Rfam database...	0.44	0.42	0.46	13	4725	17	0	15	2	18
SRP_00347	Metazoa_SRP links to Rfam database...	0.90	0.83	0.96	80	46582	12	0	3	9	16
SRP_00350	Bacteria_small_SRP links to Rfam database...	0.84	0.78	0.91	21	3893	4	1	1	2	6
SRP_00356	Bacteria_small_SRP links to Rfam database...	0.80	0.73	0.88	22	5025	6	0	3	3	8
SRP_00357	Bacteria_small_SRP links to Rfam database...	0.82	0.72	0.93	26	5328	4	1	1	2	10
SRP_00358	Bacteria_small_SRP links to Rfam database...	0.81	0.71	0.93	25	6301	5	1	1	3	10
SRP_00367	Bacteria_small_SRP links to Rfam database...	0.79	0.69	0.92	24	6760	6	1	1	4	11
SRP_00368	Metazoa_SRP links to Rfam database...	0.93	0.87	1.00	85	43871	7	0	0	7	13
SRP_00369	Bacteria_small_SRP links to Rfam database...	0.78	0.66	0.92	23	5753	7	1	1	5	12
SRP_00383	Bacteria_small_SRP links to Rfam database...	0.92	0.92	0.92	22	3216	6	0	2	4	2

^top

Performance of RNASampler(20) - scored lower in this pairwise comparison

1. Total counts & total scores for RNASampler(20)

Total Base Pair Counts
Total TP	2750
Total TN	2343690
Total FP	493
Total FP CONTRA	38
Total FP INCONS	274
Total FP COMP	181
Total FN	4325

Total Scores
MCC	0.590
Average MCC ± 95% Confidence Intervals	0.575 ± 0.041
Sensitivity	0.389
Positive Predictive Value	0.898
Nr of predictions	178

^top

2. Individual counts for RNASampler(20) [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
ASE_00064	RNaseP_bact_a links to Rfam database...	0.44	0.34	0.58	30	45399	23	1	21	1	59
ASE_00090	RNaseP_bact_a links to Rfam database...	0.54	0.40	0.74	40	55557	14	0	14	0	61
ASE_00135	RNaseP_bact_a links to Rfam database...	0.54	0.36	0.83	39	63143	16	0	8	8	70
ASE_00153	RNaseP_nuc links to Rfam database...	0.38	0.33	0.44	24	57576	38	7	23	8	49
ASE_00215	RNaseP_bact_a links to Rfam database...	0.38	0.23	0.62	23	48479	16	0	14	2	76
ASE_00305	RNaseP_bact_b links to Rfam database...	0.78	0.71	0.86	60	54545	14	1	9	4	25
ASE_00328	RNaseP_bact_b links to Rfam database...	0.70	0.57	0.85	64	72696	14	5	6	3	48
ASE_00361	RNaseP_bact_a links to Rfam database...	0.34	0.21	0.55	27	75417	26	3	19	4	100
ASE_00427	RNaseP_nuc links to Rfam database...	0.57	0.46	0.72	21	40726	18	1	7	10	25
ASE_00441	RNaseP_bact_a links to Rfam database...	0.46	0.31	0.69	35	64210	16	0	16	0	77
PDB_00012	mir-TAR links to Rfam database...	1.00	1.00	1.00	7	399	2	0	0	2	0
PDB_00213	Gammaretro_CES links to Rfam database...	0.75	0.56	1.00	23	5027	0	0	0	0	18
PDB_00553	mir-TAR links to Rfam database...	1.00	1.00	1.00	11	454	0	0	0	0	0
PDB_00741	Entero_5_CRE links to Rfam database...	0.72	0.53	1.00	9	694	0	0	0	0	8
PDB_00810	s2m links to Rfam database...	0.59	0.35	1.00	6	1075	0	0	0	0	11
PDB_00828	Purine links to Rfam database...	0.86	0.74	1.00	20	2465	0	0	0	0	7
PDB_00829	Purine links to Rfam database...	0.86	0.75	1.00	18	2260	0	0	0	0	6
PDB_00876	HIV_FE links to Rfam database...	0.92	0.90	0.95	18	971	1	0	1	0	2
PDB_01020	Purine links to Rfam database...	0.86	0.74	1.00	17	2261	1	0	0	1	6
PDB_01050	UnaL2 links to Rfam database...	0.92	0.85	1.00	11	619	2	0	0	2	2
PDB_01073	SAM links to Rfam database...	0.77	0.59	1.00	20	4351	1	0	0	1	14
PDB_01114	TPP links to Rfam database...	0.60	0.48	0.76	13	2833	4	0	4	0	14
PDB_01152	HIV_FS2 links to Rfam database...	0.84	0.71	1.00	10	551	0	0	0	0	4
PDB_01236	ykoK links to Rfam database...	0.79	0.67	0.95	36	11590	3	0	2	1	18
RFA_00389	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00390	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00391	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1418	2	0	0	2	2
RFA_00396	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	2	0	0	2	1
RFA_00402	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	0	0	0	0	0
RFA_00409	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1418	1	0	0	1	2
RFA_00416	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1470	2	0	0	2	0
RFA_00433	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00434	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00436	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00440	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1470	2	0	0	2	0
RFA_00442	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00444	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1525	0	0	0	0	0
RFA_00583	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4935	10	0	0	10	0
RFA_00584	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	2911	8	0	0	8	0
RFA_00585	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	8	0	0	8	0
RFA_00586	Y_RNA links to Rfam database...	0.89	0.80	1.00	12	3904	1	0	0	1	3
RFA_00587	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	8	0	0	8	0
RFA_00588	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4545	8	0	0	8	0
RFA_00589	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4356	7	0	0	7	0
RFA_00594	Y_RNA links to Rfam database...	0.93	0.87	1.00	13	2762	5	0	0	5	2
RFA_00596	Y_RNA links to Rfam database...	0.82	0.67	1.00	10	5985	13	0	0	13	5
RFA_00658	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1125	5	0	3	2	14
RFA_00664	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00667	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	986	5	0	4	1	14
RFA_00668	Hammerhead_1 links to Rfam database...	0.53	0.29	1.00	4	986	0	0	0	0	10
RFA_00672	Hammerhead_1 links to Rfam database...	0.41	0.31	0.57	4	896	3	0	3	0	9
RFA_00673	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1125	4	0	3	1	14
RFA_00674	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1128	0	0	0	0	14
RFA_00675	Hammerhead_1 links to Rfam database...	0.53	0.29	1.00	4	986	0	0	0	0	10
RFA_00677	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00678	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	943	3	0	3	0	14
RFA_00680	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1128	0	0	0	0	14
RFA_00704	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	987	4	0	3	1	14
RFA_00707	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1035	0	0	0	0	14
RFA_00715	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	946	0	0	0	0	14
RFA_00717	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	903	0	0	0	0	14
RFA_00730	s2m links to Rfam database...	0.81	0.67	1.00	8	895	1	0	0	1	4
RFA_00731	s2m links to Rfam database...	0.81	0.67	1.00	8	895	1	0	0	1	4
RFA_00733	s2m links to Rfam database...	0.64	0.42	1.00	5	898	1	0	0	1	7
RFA_00734	s2m links to Rfam database...	0.64	0.42	1.00	5	898	0	0	0	0	7
RFA_00736	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00737	s2m links to Rfam database...	0.81	0.67	1.00	8	895	1	0	0	1	4
RFA_00745	s2m links to Rfam database...	0.50	0.25	1.00	3	943	0	0	0	0	9
RFA_00749	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00758	s2m links to Rfam database...	0.76	0.58	1.00	7	896	0	0	0	0	5
RFA_00762	s2m links to Rfam database...	0.50	0.25	1.00	3	900	0	0	0	0	9
RFA_00763	s2m links to Rfam database...	0.81	0.67	1.00	8	895	1	0	0	1	4
RFA_00764	s2m links to Rfam database...	0.81	0.67	1.00	8	895	1	0	0	1	4
RFA_00765	s2m links to Rfam database...	0.81	0.67	1.00	8	895	1	0	0	1	4
RFA_00786	Gammaretro_CES links to Rfam database...	0.72	0.63	0.83	20	5026	4	2	2	0	12
RFA_00791	Gammaretro_CES links to Rfam database...	0.71	0.56	0.90	18	5131	2	0	2	0	14
RFA_00792	Gammaretro_CES links to Rfam database...	0.81	0.72	0.92	23	5025	2	0	2	0	9
RFA_00801	Gammaretro_CES links to Rfam database...	0.74	0.63	0.87	20	5027	3	0	3	0	12
SPR_00273	tRNA links to Rfam database...	1.00	1.00	1.00	21	2829	0	0	0	0	0
SPR_00277	tRNA links to Rfam database...	1.00	1.00	1.00	21	2905	0	0	0	0	0
SPR_00721	tRNA links to Rfam database...	1.00	1.00	1.00	21	2905	2	0	0	2	0
SPR_01157	tRNA links to Rfam database...	0.95	0.95	0.95	20	2754	2	0	1	1	1
SRP_00006	Metazoa_SRP links to Rfam database...	0.87	0.76	0.99	77	45675	4	0	1	3	24
SRP_00008	Bacteria_small_SRP links to Rfam database...	0.66	0.44	1.00	11	2915	0	0	0	0	14
SRP_00011	Plant_SRP links to Rfam database...	0.55	0.42	0.71	44	46298	18	4	14	0	60
SRP_00015	Plant_SRP links to Rfam database...	0.74	0.59	0.94	58	46298	5	3	1	1	41
SRP_00020	Bacteria_small_SRP links to Rfam database...	0.46	0.21	1.00	7	5558	0	0	0	0	26
SRP_00024	Bacteria_large_SRP links to Rfam database...	0.28	0.08	1.00	7	37668	0	0	0	0	80
SRP_00026	Bacteria_large_SRP links to Rfam database...	0.51	0.27	0.96	24	36831	1	0	1	0	64
SRP_00030	Bacteria_large_SRP links to Rfam database...	0.28	0.08	1.00	7	36849	0	0	0	0	81
SRP_00031	Bacteria_large_SRP links to Rfam database...	0.35	0.12	1.00	11	36304	0	0	0	0	78
SRP_00037	Bacteria_large_SRP links to Rfam database...	0.00	0.00	0.00	0	36585	0	0	0	0	87
SRP_00038	Bacteria_small_SRP links to Rfam database...	0.46	0.21	1.00	7	5043	0	0	0	0	26
SRP_00042	Bacteria_small_SRP links to Rfam database...	0.64	0.48	0.86	12	3991	3	1	1	1	13
SRP_00044	Bacteria_small_SRP links to Rfam database...	0.47	0.22	1.00	7	6098	0	0	0	0	25
SRP_00046	Bacteria_small_SRP links to Rfam database...	0.47	0.22	1.00	7	4746	0	0	0	0	25
SRP_00050	Metazoa_SRP links to Rfam database...	0.86	0.76	0.99	75	44774	3	0	1	2	24
SRP_00051	Bacteria_small_SRP links to Rfam database...	0.48	0.23	1.00	7	5453	0	0	0	0	23
SRP_00054	Bacteria_small_SRP links to Rfam database...	0.47	0.22	1.00	7	5558	0	0	0	0	25
SRP_00057	Bacteria_small_SRP links to Rfam database...	0.45	0.20	1.00	7	6321	0	0	0	0	28
SRP_00058	Bacteria_small_SRP links to Rfam database...	0.45	0.21	1.00	7	5771	0	0	0	0	27
SRP_00066	Metazoa_SRP links to Rfam database...	0.81	0.66	0.99	66	45384	1	0	1	0	34
SRP_00074	Bacteria_small_SRP links to Rfam database...	0.49	0.24	1.00	7	6548	0	0	0	0	22
SRP_00075	Bacteria_small_SRP links to Rfam database...	0.45	0.21	1.00	7	5558	0	0	0	0	27
SRP_00077	Bacteria_small_SRP links to Rfam database...	0.43	0.19	1.00	7	6663	0	0	0	0	30
SRP_00084	Bacteria_small_SRP links to Rfam database...	0.45	0.21	1.00	7	5453	0	0	0	0	27
SRP_00086	Metazoa_SRP links to Rfam database...	0.87	0.77	0.99	77	44175	3	0	1	2	23
SRP_00088	Bacteria_large_SRP links to Rfam database...	0.40	0.16	1.00	14	34177	0	0	0	0	75
SRP_00089	Bacteria_large_SRP links to Rfam database...	0.00	0.00	0.00	0	35778	0	0	0	0	90
SRP_00090	Bacteria_large_SRP links to Rfam database...	0.00	0.00	0.00	0	35511	0	0	0	0	90
SRP_00094	Bacteria_small_SRP links to Rfam database...	0.52	0.42	0.67	10	4080	5	1	4	0	14
SRP_00095	Bacteria_small_SRP links to Rfam database...	0.51	0.40	0.67	10	3990	5	1	4	0	15
SRP_00098	Bacteria_small_SRP links to Rfam database...	0.30	0.16	0.55	6	6430	6	0	5	1	31
SRP_00102	Metazoa_SRP links to Rfam database...	0.86	0.77	0.95	78	44469	4	0	4	0	23
SRP_00103	Metazoa_SRP links to Rfam database...	0.80	0.64	1.00	65	45386	0	0	0	0	37
SRP_00105	Bacteria_small_SRP links to Rfam database...	0.19	0.09	0.43	3	5558	4	0	4	0	31
SRP_00107	Bacteria_small_SRP links to Rfam database...	0.24	0.16	0.38	3	3647	5	0	5	0	16
SRP_00121	Bacteria_small_SRP links to Rfam database...	0.53	0.28	1.00	7	4271	0	0	0	0	18
SRP_00128	Bacteria_small_SRP links to Rfam database...	0.44	0.19	1.00	7	6779	0	0	0	0	29
SRP_00132	Bacteria_small_SRP links to Rfam database...	0.49	0.24	1.00	7	4844	0	0	0	0	22
SRP_00134	Bacteria_large_SRP links to Rfam database...	0.49	0.28	0.89	8	5986	3	0	1	2	21
SRP_00141	Bacteria_small_SRP links to Rfam database...	0.41	0.17	1.00	7	6321	0	0	0	0	34
SRP_00152	Plant_SRP links to Rfam database...	0.52	0.27	1.00	28	45725	0	0	0	0	75
SRP_00161	Bacteria_small_SRP links to Rfam database...	0.56	0.32	1.00	7	2843	0	0	0	0	15
SRP_00162	Bacteria_small_SRP links to Rfam database...	0.55	0.30	1.00	7	2919	0	0	0	0	16
SRP_00163	Bacteria_small_SRP links to Rfam database...	0.52	0.27	1.00	7	3479	0	0	0	0	19
SRP_00164	Bacteria_small_SRP links to Rfam database...	0.45	0.20	1.00	7	6896	0	0	0	0	28
SRP_00170	Bacteria_small_SRP links to Rfam database...	0.64	0.48	0.86	12	4081	3	1	1	1	13
SRP_00171	Metazoa_SRP links to Rfam database...	0.74	0.61	0.89	54	45390	7	2	5	0	34
SRP_00178	Plant_SRP links to Rfam database...	0.36	0.13	1.00	13	45740	0	0	0	0	89
SRP_00179	Plant_SRP links to Rfam database...	0.39	0.16	0.94	17	46038	1	0	1	0	88
SRP_00181	Plant_SRP links to Rfam database...	0.41	0.17	1.00	17	46039	0	0	0	0	85
SRP_00182	Plant_SRP links to Rfam database...	0.78	0.66	0.92	67	45983	6	0	6	0	34
SRP_00188	Plant_SRP links to Rfam database...	0.26	0.14	0.48	11	31102	12	1	11	0	68
SRP_00194	Bacteria_small_SRP links to Rfam database...	0.53	0.29	1.00	6	3234	0	0	0	0	15
SRP_00200	Bacteria_small_SRP links to Rfam database...	0.44	0.19	1.00	7	6896	0	0	0	0	29
SRP_00209	Bacteria_small_SRP links to Rfam database...	0.30	0.19	0.50	5	4646	5	0	5	0	22
SRP_00213	Bacteria_small_SRP links to Rfam database...	0.67	0.52	0.87	13	4171	2	1	1	0	12
SRP_00215	Bacteria_small_SRP links to Rfam database...	0.53	0.28	1.00	7	3233	0	0	0	0	18
SRP_00227	Bacteria_small_SRP links to Rfam database...	0.59	0.35	1.00	11	5140	0	0	0	0	20
SRP_00228	Metazoa_SRP links to Rfam database...	0.88	0.78	0.99	74	45376	7	0	1	6	21
SRP_00231	Bacteria_small_SRP links to Rfam database...	0.45	0.21	1.00	7	5453	0	0	0	0	27
SRP_00233	Bacteria_small_SRP links to Rfam database...	0.35	0.12	1.00	4	5147	0	0	0	0	29
SRP_00234	Bacteria_large_SRP links to Rfam database...	0.47	0.23	0.95	20	36294	1	0	1	0	66
SRP_00243	Bacteria_small_SRP links to Rfam database...	0.47	0.23	1.00	7	5144	0	0	0	0	24
SRP_00244	Bacteria_small_SRP links to Rfam database...	0.42	0.18	1.00	7	6896	0	0	0	0	32
SRP_00250	Bacteria_small_SRP links to Rfam database...	0.44	0.19	1.00	7	6779	0	0	0	0	29
SRP_00251	Bacteria_small_SRP links to Rfam database...	0.44	0.19	1.00	7	7014	0	0	0	0	29
SRP_00266	Bacteria_small_SRP links to Rfam database...	0.49	0.24	1.00	7	4649	0	0	0	0	22
SRP_00268	Bacteria_small_SRP links to Rfam database...	0.72	0.59	0.89	16	4168	2	1	1	0	11
SRP_00269	Bacteria_small_SRP links to Rfam database...	0.55	0.30	1.00	10	5040	0	0	0	0	23
SRP_00270	Bacteria_small_SRP links to Rfam database...	0.27	0.13	0.57	4	4649	3	0	3	0	27
SRP_00271	Bacteria_small_SRP links to Rfam database...	0.54	0.29	1.00	7	3233	0	0	0	0	17
SRP_00273	Bacteria_small_SRP links to Rfam database...	0.52	0.28	1.00	11	6775	0	0	0	0	29
SRP_00274	Bacteria_small_SRP links to Rfam database...	0.43	0.18	1.00	7	6896	0	0	0	0	31
SRP_00295	Bacteria_small_SRP links to Rfam database...	0.40	0.16	1.00	6	6897	0	0	0	0	32
SRP_00303	Bacteria_small_SRP links to Rfam database...	0.19	0.09	0.38	3	6662	5	0	5	0	29
SRP_00308	Bacteria_large_SRP links to Rfam database...	0.28	0.08	1.00	7	36308	0	0	0	0	81
SRP_00312	Bacteria_small_SRP links to Rfam database...	0.49	0.37	0.67	10	4171	5	1	4	0	17
SRP_00315	Bacteria_small_SRP links to Rfam database...	0.55	0.30	1.00	7	2919	0	0	0	0	16
SRP_00317	Metazoa_SRP links to Rfam database...	0.76	0.61	0.95	60	45087	8	0	3	5	38
SRP_00318	Bacteria_small_SRP links to Rfam database...	0.55	0.30	1.00	7	2996	0	0	0	0	16
SRP_00325	Bacteria_small_SRP links to Rfam database...	0.46	0.21	1.00	7	4364	0	0	0	0	26
SRP_00326	Bacteria_small_SRP links to Rfam database...	0.27	0.13	0.57	4	5043	3	0	3	0	27
SRP_00333	Bacteria_small_SRP links to Rfam database...	0.45	0.21	1.00	7	5144	0	0	0	0	27
SRP_00335	Bacteria_large_SRP links to Rfam database...	0.42	0.18	1.00	7	35238	0	0	0	0	32
SRP_00337	Bacteria_large_SRP links to Rfam database...	0.38	0.14	1.00	13	35498	0	0	0	0	78
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.44	0.19	1.00	7	5453	0	0	0	0	29
SRP_00341	Bacteria_small_SRP links to Rfam database...	0.47	0.23	1.00	7	4746	0	0	0	0	24
SRP_00347	Metazoa_SRP links to Rfam database...	0.80	0.66	0.98	63	46601	5	0	1	4	33
SRP_00350	Bacteria_small_SRP links to Rfam database...	0.62	0.44	0.86	12	3902	2	1	1	0	15
SRP_00356	Bacteria_small_SRP links to Rfam database...	0.48	0.23	1.00	7	5043	0	0	0	0	23
SRP_00357	Bacteria_small_SRP links to Rfam database...	0.55	0.31	1.00	11	5345	0	0	0	0	25
SRP_00358	Bacteria_small_SRP links to Rfam database...	0.45	0.20	1.00	7	6321	0	0	0	0	28
SRP_00367	Bacteria_small_SRP links to Rfam database...	0.45	0.20	1.00	7	6779	0	0	0	0	28
SRP_00368	Metazoa_SRP links to Rfam database...	0.77	0.59	1.00	58	43898	2	0	0	2	40
SRP_00369	Bacteria_small_SRP links to Rfam database...	0.45	0.20	1.00	7	5771	0	0	0	0	28
SRP_00383	Bacteria_small_SRP links to Rfam database...	0.54	0.29	1.00	7	3233	0	0	0	0	17

^top

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

Table of contents:

Overview

Performance plots

Performance of CentroidAlifold(seed) - scored higher in this pairwise comparison

1. Total counts & total scores for CentroidAlifold(seed)

2. Individual counts for CentroidAlifold(seed) [ download as .csv ]

Performance of RNASampler(20) - scored lower in this pairwise comparison

1. Total counts & total scores for RNASampler(20)

2. Individual counts for RNASampler(20) [ download as .csv ]