CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	CMfinder(20)		NanoFolder
MCC	0.525	>	0.187
Average MCC ± 95% Confidence Intervals	0.576 ± 0.043	>	0.256 ± 0.038
Sensitivity	0.353	>	0.216
Positive Predictive Value	0.783	>	0.165
Total TP	2585	>	1579
Total TN	3518114	>	3511864
Total FP	824	<	8169
Total FP CONTRA	61	<	1204
Total FP INCONS	657	<	6770
Total FP COMP	106	<	195
Total FN	4737	<	5743
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of CMfinder(20) and NanoFolder. 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 CMfinder(20) and NanoFolder).
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 CMfinder(20) and NanoFolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for CMfinder(20) and NanoFolder. 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 CMfinder(20) and NanoFolder).

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Performance of CMfinder(20) - scored higher in this pairwise comparison

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

Total Base Pair Counts
Total TP	2585
Total TN	3518114
Total FP	824
Total FP CONTRA	61
Total FP INCONS	657
Total FP COMP	106
Total FN	4737

Total Scores
MCC	0.525
Average MCC ± 95% Confidence Intervals	0.576 ± 0.043
Sensitivity	0.353
Positive Predictive Value	0.783
Nr of predictions	114

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
ASE_00083	RNaseP_bact_a links to Rfam database...	0.50	0.27	0.91	30	62448	4	0	3	1	80
ASE_00185	RNaseP_bact_a links to Rfam database...	0.35	0.18	0.70	23	73503	10	0	10	0	105
ASE_00190	RNaseP_bact_b links to Rfam database...	0.32	0.18	0.57	16	45423	13	1	11	1	74
ASE_00221	RNaseP_bact_a links to Rfam database...	0.56	0.38	0.80	45	64564	11	1	10	0	72
ASE_00228	RNaseP_bact_a links to Rfam database...	0.41	0.24	0.70	21	46941	10	2	7	1	65
ASE_00229	RNaseP_bact_a links to Rfam database...	0.57	0.44	0.75	38	42435	14	0	13	1	49
ASE_00231	RNaseP_bact_a links to Rfam database...	0.61	0.45	0.83	43	47843	9	2	7	0	53
ASE_00234	RNaseP_bact_a links to Rfam database...	0.45	0.27	0.74	35	75419	12	1	11	0	94
ASE_00238	RNaseP_bact_a links to Rfam database...	0.46	0.22	0.96	25	64235	1	0	1	0	89
ASE_00248	RNaseP_bact_a links to Rfam database...	0.56	0.39	0.80	44	62426	11	1	10	0	70
ASE_00254	RNaseP_bact_a links to Rfam database...	0.65	0.55	0.76	45	36797	14	3	11	0	37
ASE_00255	RNaseP_bact_a links to Rfam database...	0.42	0.22	0.82	28	74657	6	1	5	0	102
ASE_00257	RNaseP_bact_a links to Rfam database...	0.51	0.36	0.73	35	50992	14	0	13	1	62
ASE_00267	RNaseP_bact_a links to Rfam database...	0.62	0.47	0.82	41	45100	10	0	9	1	47
ASE_00270	RNaseP_bact_a links to Rfam database...	0.47	0.27	0.80	35	72346	9	0	9	0	93
ASE_00274	RNaseP_bact_a links to Rfam database...	0.56	0.42	0.75	43	55554	14	1	13	0	60
ASE_00277	RNaseP_bact_a links to Rfam database...	0.49	0.27	0.89	25	48177	3	0	3	0	66
ASE_00279	RNaseP_bact_a links to Rfam database...	0.50	0.27	0.93	27	53272	2	0	2	0	74
ASE_00285	RNaseP_bact_a links to Rfam database...	0.43	0.22	0.82	27	68973	6	0	6	0	95
ASE_00287	RNaseP_bact_a links to Rfam database...	0.44	0.31	0.63	32	54895	20	1	18	1	71
ASE_00294	RNaseP_bact_a links to Rfam database...	0.37	0.19	0.74	32	114438	12	0	11	1	139
ASE_00298	RNaseP_bact_a links to Rfam database...	0.54	0.38	0.75	43	67471	14	1	13	0	70
ASE_00318	RNaseP_bact_b links to Rfam database...	0.49	0.31	0.80	36	80155	10	3	6	1	82
ASE_00321	RNaseP_bact_b links to Rfam database...	0.54	0.41	0.72	36	54565	15	1	13	1	52
ASE_00335	RNaseP_bact_b links to Rfam database...	0.46	0.32	0.67	37	75411	19	2	16	1	79
ASE_00340	RNaseP_bact_a links to Rfam database...	0.47	0.36	0.62	31	46006	19	5	14	0	54
ASE_00367	RNaseP_bact_a links to Rfam database...	0.50	0.30	0.84	26	43040	5	0	5	0	60
ASE_00370	RNaseP_bact_a links to Rfam database...	0.69	0.57	0.83	48	41847	11	1	9	1	36
ASE_00372	RNaseP_bact_a links to Rfam database...	0.60	0.43	0.84	43	51952	8	0	8	0	57
ASE_00376	RNaseP_bact_a links to Rfam database...	0.42	0.25	0.70	26	56916	11	0	11	0	79
ASE_00377	RNaseP_bact_a links to Rfam database...	0.43	0.25	0.75	27	57594	10	0	9	1	80
ASE_00386	RNaseP_bact_a links to Rfam database...	0.54	0.31	0.94	30	50371	3	0	2	1	66
ASE_00393	RNaseP_bact_a links to Rfam database...	0.58	0.45	0.74	42	47838	15	1	14	0	51
ASE_00412	RNaseP_bact_a links to Rfam database...	0.53	0.36	0.79	38	58263	11	0	10	1	67
ASE_00413	RNaseP_bact_a links to Rfam database...	0.51	0.37	0.70	30	44508	14	3	10	1	51
ASE_00416	RNaseP_bact_a links to Rfam database...	0.42	0.21	0.82	27	77388	7	0	6	1	100
ASE_00422	RNaseP_bact_a links to Rfam database...	0.57	0.40	0.79	38	46923	11	0	10	1	56
ASE_00427	RNaseP_nuc links to Rfam database...	0.37	0.30	0.45	14	40724	41	4	13	24	32
ASE_00428	RNaseP_bact_a links to Rfam database...	0.56	0.40	0.79	50	76573	13	1	12	0	75
ASE_00430	RNaseP_bact_a links to Rfam database...	0.46	0.25	0.86	24	46943	4	0	4	0	73
ASE_00437	RNaseP_bact_a links to Rfam database...	0.58	0.39	0.87	53	79340	8	0	8	0	82
ASE_00451	RNaseP_bact_a links to Rfam database...	0.54	0.35	0.83	44	70823	10	1	8	1	81
CRW_01535	5S_rRNA links to Rfam database...	0.68	0.51	0.90	19	7119	2	0	2	0	18
CRW_01539	5S_rRNA links to Rfam database...	0.72	0.65	0.80	24	7110	12	0	6	6	13
CRW_01563	5S_rRNA links to Rfam database...	0.68	0.51	0.90	19	6882	3	0	2	1	18
CRW_01583	5S_rRNA links to Rfam database...	0.81	0.70	0.93	26	7112	3	0	2	1	11
CRW_01590	5S_rRNA links to Rfam database...	0.76	0.62	0.92	23	7115	3	0	2	1	14
CRW_01593	5S_rRNA links to Rfam database...	0.68	0.51	0.90	19	7119	4	0	2	2	18
CRW_01595	5S_rRNA links to Rfam database...	0.68	0.62	0.74	23	8484	11	0	8	3	14
CRW_01603	5S_rRNA links to Rfam database...	0.62	0.43	0.89	16	7122	2	0	2	0	21
CRW_01617	5S_rRNA links to Rfam database...	0.74	0.62	0.88	23	7114	6	0	3	3	14
CRW_01625	5S_rRNA links to Rfam database...	0.76	0.62	0.92	23	7115	2	0	2	0	14
PDB_00070	tRNA links to Rfam database...	0.76	0.58	1.00	14	2836	0	0	0	0	10
PDB_00571	tRNA links to Rfam database...	0.87	0.80	0.95	20	3300	1	0	1	0	5
PDB_00828	Purine links to Rfam database...	0.84	0.70	1.00	19	2466	0	0	0	0	8
PDB_01236	ykoK links to Rfam database...	0.54	0.41	0.71	22	11597	10	0	9	1	32
RFA_00416	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1472	1	0	0	1	2
RFA_00434	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1418	1	0	0	1	2
RFA_00436	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1418	1	0	0	1	2
RFA_00442	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1418	1	0	0	1	2
RFA_00664	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	985	5	0	5	0	14
RFA_00674	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1123	5	0	5	0	14
RFA_00675	Hammerhead_1 links to Rfam database...	0.35	0.21	0.60	3	985	3	0	2	1	11
RFA_00677	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	985	5	0	5	0	14
RFA_00717	Hammerhead_1 links to Rfam database...	0.46	0.21	1.00	3	900	0	0	0	0	11
RFA_00730	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00763	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00765	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
SPR_00066	tRNA links to Rfam database...	0.95	0.90	1.00	19	2831	0	0	0	0	2
SPR_00314	tRNA links to Rfam database...	0.98	0.95	1.00	20	2906	0	0	0	0	1
SPR_00333	tRNA links to Rfam database...	0.58	0.52	0.65	11	2758	6	0	6	0	10
SPR_00353	tRNA links to Rfam database...	0.82	0.67	1.00	14	2836	0	0	0	0	7
SPR_00452	tRNA links to Rfam database...	0.98	0.95	1.00	20	2830	0	0	0	0	1
SPR_00456	tRNA links to Rfam database...	0.93	0.86	1.00	18	2832	0	0	0	0	3
SPR_00476	tRNA links to Rfam database...	0.56	0.43	0.75	9	2763	3	1	2	0	12
SPR_00496	tRNA links to Rfam database...	0.82	0.67	1.00	14	2761	0	0	0	0	7
SPR_00497	tRNA links to Rfam database...	0.82	0.67	1.00	14	2761	0	0	0	0	7
SPR_00502	tRNA links to Rfam database...	0.93	0.86	1.00	18	2908	0	0	0	0	3
SPR_00509	tRNA links to Rfam database...	0.92	0.85	1.00	17	2909	0	0	0	0	3
SPR_00512	tRNA links to Rfam database...	0.78	0.70	0.88	14	2910	2	0	2	0	6
SPR_00557	tRNA links to Rfam database...	0.95	0.90	1.00	19	2831	0	0	0	0	2
SPR_00868	tRNA links to Rfam database...	0.95	0.90	1.00	19	2907	0	0	0	0	2
SPR_00957	tRNA links to Rfam database...	0.98	0.95	1.00	20	2983	0	0	0	0	1
SPR_01040	tRNA links to Rfam database...	0.93	0.86	1.00	18	2757	0	0	0	0	3
SRP_00038	Bacteria_small_SRP links to Rfam database...	0.22	0.21	0.24	7	5021	22	0	22	0	26
SRP_00046	Bacteria_small_SRP links to Rfam database...	0.47	0.22	1.00	7	4746	0	0	0	0	25
SRP_00103	Metazoa_SRP links to Rfam database...	0.31	0.23	0.42	23	45396	32	0	32	0	79
SRP_00170	Bacteria_small_SRP links to Rfam database...	0.48	0.40	0.59	10	4078	7	1	6	0	15
SRP_00173	Bacteria_large_SRP links to Rfam database...	0.49	0.27	0.89	24	38199	3	0	3	0	66
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...	0.27	0.11	0.67	4	6897	2	0	2	0	32
SRP_00233	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5140	11	1	10	0	33
SRP_00234	Bacteria_large_SRP links to Rfam database...	0.19	0.03	1.00	3	36312	0	0	0	0	83
SRP_00266	Bacteria_small_SRP links to Rfam database...	0.63	0.59	0.68	17	4631	9	1	7	1	12
SRP_00269	Bacteria_small_SRP links to Rfam database...	0.76	0.58	1.00	19	5031	0	0	0	0	14
SRP_00273	Bacteria_small_SRP links to Rfam database...	0.71	0.58	0.88	23	6760	3	1	2	0	17
SRP_00303	Bacteria_small_SRP links to Rfam database...	0.69	0.56	0.86	18	6649	3	0	3	0	14
SRP_00308	Bacteria_large_SRP links to Rfam database...	0.41	0.26	0.66	23	36280	12	1	11	0	65
SRP_00317	Metazoa_SRP links to Rfam database...	0.63	0.43	0.93	42	45105	3	0	3	0	56
SRP_00333	Bacteria_small_SRP links to Rfam database...	0.38	0.15	1.00	5	5146	0	0	0	0	29
SRP_00337	Bacteria_large_SRP links to Rfam database...	0.44	0.30	0.66	27	35470	15	3	11	1	64
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.93	0.89	0.97	32	5427	1	0	1	0	4
SRP_00342	Bacteria_small_SRP links to Rfam database...	0.49	0.24	1.00	6	3999	0	0	0	0	19
SRP_00358	Bacteria_small_SRP links to Rfam database...	0.53	0.29	1.00	10	6318	0	0	0	0	25
SRP_00383	Bacteria_small_SRP links to Rfam database...	0.43	0.29	0.64	7	3229	4	0	4	0	17
TMR_00123	tmRNA links to Rfam database...	0.41	0.22	0.76	22	66401	12	0	7	5	79
TMR_00399	tmRNA links to Rfam database...	0.18	0.09	0.36	8	64958	14	7	7	0	86
TMR_00443	tmRNA links to Rfam database...	0.41	0.27	0.64	28	67117	20	1	15	4	76
TMR_00469	tmRNA links to Rfam database...	0.50	0.31	0.79	31	64581	12	1	7	4	69
TMR_00519	tmRNA links to Rfam database...	0.28	0.18	0.44	17	63151	27	2	20	5	78
TMR_00528	tmRNA links to Rfam database...	0.40	0.23	0.71	22	63159	13	2	7	4	75
TMR_00571	tmRNA links to Rfam database...	0.37	0.19	0.70	19	60699	13	0	8	5	80
TMR_00584	tmRNA links to Rfam database...	0.31	0.15	0.63	15	61051	15	1	8	6	82
TMR_00703	tmRNA links to Rfam database...	0.52	0.35	0.78	35	67483	15	1	9	5	64

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Performance of NanoFolder - scored lower in this pairwise comparison

1. Total counts & total scores for NanoFolder

Total Base Pair Counts
Total TP	1579
Total TN	3511864
Total FP	8169
Total FP CONTRA	1204
Total FP INCONS	6770
Total FP COMP	195
Total FN	5743

Total Scores
MCC	0.187
Average MCC ± 95% Confidence Intervals	0.256 ± 0.038
Sensitivity	0.216
Positive Predictive Value	0.165
Nr of predictions	114

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2. Individual counts for NanoFolder [ download as .csv ]

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
ASE_00083	RNaseP_bact_a links to Rfam database...	0.22	0.25	0.20	27	62347	108	12	95	1	83
ASE_00185	RNaseP_bact_a links to Rfam database...	0.17	0.19	0.16	24	73382	134	14	116	4	104
ASE_00190	RNaseP_bact_b links to Rfam database...	0.24	0.28	0.21	25	45334	93	14	78	1	65
ASE_00221	RNaseP_bact_a links to Rfam database...	0.20	0.21	0.18	25	64484	112	10	101	1	92
ASE_00228	RNaseP_bact_a links to Rfam database...	0.05	0.06	0.04	5	46858	109	17	91	1	81
ASE_00229	RNaseP_bact_a links to Rfam database...	0.12	0.14	0.11	12	42380	97	12	82	3	75
ASE_00231	RNaseP_bact_a links to Rfam database...	0.37	0.42	0.33	40	47773	84	17	65	2	56
ASE_00234	RNaseP_bact_a links to Rfam database...	0.25	0.27	0.23	35	75315	117	10	106	1	94
ASE_00238	RNaseP_bact_a links to Rfam database...	0.26	0.30	0.23	34	64111	119	18	98	3	80
ASE_00248	RNaseP_bact_a links to Rfam database...	0.13	0.15	0.12	17	62340	124	9	115	0	97
ASE_00254	RNaseP_bact_a links to Rfam database...	0.15	0.16	0.14	13	36761	88	3	79	6	69
ASE_00255	RNaseP_bact_a links to Rfam database...	0.11	0.12	0.10	16	74530	146	16	129	1	114
ASE_00257	RNaseP_bact_a links to Rfam database...	0.37	0.42	0.33	41	50917	85	15	67	3	56
ASE_00267	RNaseP_bact_a links to Rfam database...	0.00	0.00	0.00	0	45036	115	9	105	1	88
ASE_00270	RNaseP_bact_a links to Rfam database...	0.19	0.21	0.17	27	72232	132	14	117	1	101
ASE_00274	RNaseP_bact_a links to Rfam database...	0.00	0.00	0.00	0	55487	126	12	112	2	103
ASE_00277	RNaseP_bact_a links to Rfam database...	0.10	0.12	0.08	11	48071	123	23	100	0	80
ASE_00279	RNaseP_bact_a links to Rfam database...	0.14	0.16	0.13	16	53177	109	16	92	1	85
ASE_00285	RNaseP_bact_a links to Rfam database...	0.34	0.36	0.31	44	68866	98	14	82	2	78
ASE_00287	RNaseP_bact_a links to Rfam database...	0.15	0.17	0.14	17	54824	107	14	91	2	86
ASE_00294	RNaseP_bact_a links to Rfam database...	0.12	0.13	0.12	23	114287	172	11	160	1	148
ASE_00298	RNaseP_bact_a links to Rfam database...	0.09	0.10	0.08	11	67389	129	8	120	1	102
ASE_00318	RNaseP_bact_b links to Rfam database...	0.03	0.04	0.03	5	80039	156	21	135	0	113
ASE_00321	RNaseP_bact_b links to Rfam database...	0.11	0.14	0.09	12	54484	122	22	97	3	76
ASE_00335	RNaseP_bact_b links to Rfam database...	0.10	0.12	0.09	14	75304	151	22	126	3	102
ASE_00340	RNaseP_bact_a links to Rfam database...	0.06	0.07	0.05	6	45943	110	13	94	3	79
ASE_00367	RNaseP_bact_a links to Rfam database...	0.08	0.09	0.07	8	42960	110	10	93	7	78
ASE_00370	RNaseP_bact_a links to Rfam database...	0.03	0.04	0.03	3	41796	109	18	88	3	81
ASE_00372	RNaseP_bact_a links to Rfam database...	0.17	0.20	0.15	20	51871	113	19	93	1	80
ASE_00376	RNaseP_bact_a links to Rfam database...	0.00	0.00	0.00	0	56822	136	9	122	5	105
ASE_00377	RNaseP_bact_a links to Rfam database...	0.25	0.27	0.23	29	57505	98	10	86	2	78
ASE_00386	RNaseP_bact_a links to Rfam database...	0.14	0.16	0.13	15	50284	106	9	95	2	81
ASE_00393	RNaseP_bact_a links to Rfam database...	0.31	0.35	0.27	33	47773	90	18	71	1	60
ASE_00412	RNaseP_bact_a links to Rfam database...	0.15	0.17	0.14	18	58183	111	14	96	1	87
ASE_00413	RNaseP_bact_a links to Rfam database...	0.08	0.10	0.07	8	44438	108	19	86	3	73
ASE_00416	RNaseP_bact_a links to Rfam database...	0.39	0.43	0.35	54	77267	103	18	82	3	73
ASE_00422	RNaseP_bact_a links to Rfam database...	0.28	0.31	0.25	29	46856	87	9	77	1	65
ASE_00427	RNaseP_nuc links to Rfam database...	0.06	0.09	0.04	4	40651	105	35	65	5	42
ASE_00428	RNaseP_bact_a links to Rfam database...	0.24	0.26	0.22	33	76483	121	13	107	1	92
ASE_00430	RNaseP_bact_a links to Rfam database...	0.16	0.18	0.14	17	46852	102	10	92	0	80
ASE_00437	RNaseP_bact_a links to Rfam database...	0.00	0.00	0.00	0	79238	164	12	151	1	135
ASE_00451	RNaseP_bact_a links to Rfam database...	0.20	0.22	0.19	27	70731	118	8	110	0	98
CRW_01535	5S_rRNA links to Rfam database...	0.20	0.24	0.17	9	7088	43	7	36	0	28
CRW_01539	5S_rRNA links to Rfam database...	0.10	0.11	0.10	4	7099	40	1	36	3	33
CRW_01563	5S_rRNA links to Rfam database...	0.11	0.14	0.11	5	6856	43	5	37	1	32
CRW_01583	5S_rRNA links to Rfam database...	0.36	0.41	0.33	15	7095	31	8	22	1	22
CRW_01590	5S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	7093	50	7	40	3	37
CRW_01593	5S_rRNA links to Rfam database...	0.32	0.38	0.29	14	7091	36	5	30	1	23
CRW_01595	5S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	8459	57	10	46	1	37
CRW_01603	5S_rRNA links to Rfam database...	0.41	0.46	0.38	17	7095	29	6	22	1	20
CRW_01617	5S_rRNA links to Rfam database...	0.20	0.24	0.17	9	7087	45	7	37	1	28
CRW_01625	5S_rRNA links to Rfam database...	0.43	0.49	0.38	18	7093	31	7	22	2	19
PDB_00070	tRNA links to Rfam database...	0.25	0.29	0.23	7	2819	24	4	20	0	17
PDB_00571	tRNA links to Rfam database...	-0.01	0.00	0.00	0	3286	36	6	29	1	25
PDB_00828	Purine links to Rfam database...	0.30	0.33	0.28	9	2453	23	0	23	0	18
PDB_01236	ykoK links to Rfam database...	0.31	0.33	0.30	18	11568	43	3	39	1	36
RFA_00416	Hammerhead_3 links to Rfam database...	0.94	1.00	0.88	15	1468	6	2	0	4	0
RFA_00434	Hammerhead_3 links to Rfam database...	0.84	1.00	0.71	15	1410	8	6	0	2	0
RFA_00436	Hammerhead_3 links to Rfam database...	0.86	1.00	0.75	15	1411	7	5	0	2	0
RFA_00442	Hammerhead_3 links to Rfam database...	0.94	1.00	0.88	15	1414	4	2	0	2	0
RFA_00664	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	978	13	0	12	1	14
RFA_00674	Hammerhead_1 links to Rfam database...	0.12	0.14	0.13	2	1112	15	0	14	1	12
RFA_00675	Hammerhead_1 links to Rfam database...	0.28	0.29	0.29	4	976	10	1	9	0	10
RFA_00677	Hammerhead_1 links to Rfam database...	0.62	0.64	0.60	9	975	10	0	6	4	5
RFA_00717	Hammerhead_1 links to Rfam database...	0.64	0.64	0.64	9	889	5	2	3	0	5
RFA_00730	s2m links to Rfam database...	0.38	0.42	0.36	5	889	10	3	6	1	7
RFA_00763	s2m links to Rfam database...	0.38	0.42	0.36	5	889	10	3	6	1	7
RFA_00765	s2m links to Rfam database...	0.39	0.42	0.38	5	890	9	2	6	1	7
SPR_00066	tRNA links to Rfam database...	0.47	0.57	0.39	12	2819	20	4	15	1	9
SPR_00314	tRNA links to Rfam database...	0.47	0.57	0.39	12	2895	21	9	10	2	9
SPR_00333	tRNA links to Rfam database...	0.25	0.33	0.21	7	2741	27	10	17	0	14
SPR_00353	tRNA links to Rfam database...	0.64	0.81	0.52	17	2817	16	8	8	0	4
SPR_00452	tRNA links to Rfam database...	0.27	0.33	0.23	7	2820	24	7	16	1	14
SPR_00456	tRNA links to Rfam database...	0.49	0.57	0.43	12	2822	19	5	11	3	9
SPR_00476	tRNA links to Rfam database...	0.47	0.52	0.42	11	2749	17	4	11	2	10
SPR_00496	tRNA links to Rfam database...	0.47	0.57	0.40	12	2745	22	7	11	4	9
SPR_00497	tRNA links to Rfam database...	0.27	0.33	0.23	7	2745	23	5	18	0	14
SPR_00502	tRNA links to Rfam database...	0.27	0.33	0.23	7	2896	26	2	21	3	14
SPR_00509	tRNA links to Rfam database...	0.23	0.30	0.19	6	2895	25	8	17	0	14
SPR_00512	tRNA links to Rfam database...	0.61	0.75	0.50	15	2896	15	6	9	0	5
SPR_00557	tRNA links to Rfam database...	0.42	0.52	0.34	11	2818	22	8	13	1	10
SPR_00868	tRNA links to Rfam database...	0.49	0.57	0.43	12	2898	19	5	11	3	9
SPR_00957	tRNA links to Rfam database...	0.63	0.76	0.53	16	2973	15	7	7	1	5
SPR_01040	tRNA links to Rfam database...	0.15	0.19	0.13	4	2744	27	4	23	0	17
SRP_00038	Bacteria_small_SRP links to Rfam database...	0.23	0.27	0.20	9	5005	36	1	35	0	24
SRP_00046	Bacteria_small_SRP links to Rfam database...	0.33	0.38	0.29	12	4712	30	3	26	1	20
SRP_00103	Metazoa_SRP links to Rfam database...	0.00	0.00	0.00	0	45319	132	14	118	0	102
SRP_00170	Bacteria_small_SRP links to Rfam database...	0.29	0.36	0.25	9	4059	28	4	23	1	16
SRP_00173	Bacteria_large_SRP links to Rfam database...	0.00	0.00	0.00	0	38104	124	13	109	2	90
SRP_00194	Bacteria_small_SRP links to Rfam database...	0.27	0.33	0.23	7	3209	27	5	19	3	14
SRP_00200	Bacteria_small_SRP links to Rfam database...	0.41	0.47	0.35	17	6855	31	4	27	0	19
SRP_00233	Bacteria_small_SRP links to Rfam database...	0.25	0.30	0.22	10	5106	35	4	31	0	23
SRP_00234	Bacteria_large_SRP links to Rfam database...	0.21	0.24	0.18	21	36200	97	19	75	3	65
SRP_00266	Bacteria_small_SRP links to Rfam database...	0.55	0.66	0.46	19	4615	22	8	14	0	10
SRP_00269	Bacteria_small_SRP links to Rfam database...	0.46	0.52	0.43	17	5010	24	6	17	1	16
SRP_00273	Bacteria_small_SRP links to Rfam database...	0.36	0.40	0.33	16	6737	34	6	27	1	24
SRP_00303	Bacteria_small_SRP links to Rfam database...	0.36	0.41	0.33	13	6630	27	3	24	0	19
SRP_00308	Bacteria_large_SRP links to Rfam database...	0.14	0.17	0.12	15	36189	112	18	93	1	73
SRP_00317	Metazoa_SRP links to Rfam database...	0.14	0.16	0.12	16	45018	116	16	100	0	82
SRP_00333	Bacteria_small_SRP links to Rfam database...	0.20	0.24	0.19	8	5108	35	3	32	0	26
SRP_00337	Bacteria_large_SRP links to Rfam database...	0.42	0.46	0.38	42	35400	70	15	54	1	49
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.52	0.56	0.49	20	5419	22	4	17	1	16
SRP_00342	Bacteria_small_SRP links to Rfam database...	0.20	0.24	0.17	6	3970	29	7	22	0	19
SRP_00358	Bacteria_small_SRP links to Rfam database...	0.32	0.37	0.28	13	6282	33	4	29	0	22
SRP_00383	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	3205	35	9	26	0	24
TMR_00123	tmRNA links to Rfam database...	0.19	0.23	0.16	23	66283	126	20	104	2	78
TMR_00399	tmRNA links to Rfam database...	0.20	0.26	0.16	24	64833	130	38	85	7	70
TMR_00443	tmRNA links to Rfam database...	0.17	0.20	0.15	21	67018	126	24	98	4	83
TMR_00469	tmRNA links to Rfam database...	0.10	0.12	0.08	12	64469	145	27	112	6	88
TMR_00519	tmRNA links to Rfam database...	0.04	0.05	0.03	5	63046	141	33	106	2	90
TMR_00528	tmRNA links to Rfam database...	0.13	0.15	0.11	15	63051	131	20	104	7	82
TMR_00571	tmRNA links to Rfam database...	0.05	0.06	0.04	6	60577	149	19	124	6	93
TMR_00584	tmRNA links to Rfam database...	0.01	0.01	0.01	1	60922	159	33	119	7	96
TMR_00703	tmRNA links to Rfam database...	0.10	0.12	0.08	12	67376	140	26	114	0	87

^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 CMfinder(20) - scored higher in this pairwise comparison

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

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

Performance of NanoFolder - scored lower in this pairwise comparison

1. Total counts & total scores for NanoFolder

2. Individual counts for NanoFolder [ download as .csv ]