CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	MXScarna(seed)		NanoFolder
MCC	0.664	>	0.202
Average MCC ± 95% Confidence Intervals	0.685 ± 0.037	>	0.260 ± 0.038
Sensitivity	0.566	>	0.232
Positive Predictive Value	0.780	>	0.179
Total TP	5159	>	2117
Total TN	4589888	>	4584648
Total FP	1979	<	10017
Total FP CONTRA	172	<	1492
Total FP INCONS	1283	<	8245
Total FP COMP	524	>	280
Total FN	3959	<	7001
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of MXScarna(seed) 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 MXScarna(seed) 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 MXScarna(seed) and NanoFolder).
Comparison of average Matthews Correlation Coefficients (MCCs) for MXScarna(seed) 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 MXScarna(seed) and NanoFolder).

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

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

Total Base Pair Counts
Total TP	5159
Total TN	4589888
Total FP	1979
Total FP CONTRA	172
Total FP INCONS	1283
Total FP COMP	524
Total FN	3959

Total Scores
MCC	0.664
Average MCC ± 95% Confidence Intervals	0.685 ± 0.037
Sensitivity	0.566
Positive Predictive Value	0.780
Nr of predictions	126

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
ASE_00017	RNaseP_nuc links to Rfam database...	0.49	0.41	0.59	26	50996	36	2	16	18	38
ASE_00083	RNaseP_bact_a links to Rfam database...	0.71	0.56	0.89	62	62411	11	1	7	3	48
ASE_00122	RNaseP_bact_a links to Rfam database...	0.66	0.58	0.75	51	43297	20	1	16	3	37
ASE_00185	RNaseP_bact_a links to Rfam database...	0.23	0.16	0.32	21	73470	46	8	37	1	107
ASE_00190	RNaseP_bact_b links to Rfam database...	0.53	0.42	0.67	38	45394	23	5	14	4	52
ASE_00191	RNaseP_arch links to Rfam database...	0.82	0.70	0.96	43	29601	4	0	2	2	18
ASE_00196	RNaseP_arch links to Rfam database...	0.66	0.52	0.85	39	31580	9	0	7	2	36
ASE_00221	RNaseP_bact_a links to Rfam database...	0.78	0.69	0.89	81	64529	13	2	8	3	36
ASE_00227	RNaseP_bact_a links to Rfam database...	0.28	0.21	0.38	28	78930	47	1	44	2	105
ASE_00228	RNaseP_bact_a links to Rfam database...	0.62	0.51	0.76	44	46913	18	2	12	4	42
ASE_00229	RNaseP_bact_a links to Rfam database...	0.72	0.62	0.84	54	42422	13	1	9	3	33
ASE_00231	RNaseP_bact_a links to Rfam database...	0.49	0.40	0.60	38	47832	27	5	20	2	58
ASE_00234	RNaseP_bact_a links to Rfam database...	0.23	0.17	0.32	22	75398	48	3	43	2	107
ASE_00238	RNaseP_bact_a links to Rfam database...	0.54	0.39	0.76	44	64203	17	3	11	3	70
ASE_00248	RNaseP_bact_a links to Rfam database...	0.81	0.72	0.92	82	62392	11	2	5	4	32
ASE_00250	RNaseP_bact_a links to Rfam database...	0.60	0.49	0.73	64	78915	25	4	20	1	67
ASE_00254	RNaseP_bact_a links to Rfam database...	0.67	0.59	0.77	48	36794	17	1	13	3	34
ASE_00255	RNaseP_bact_a links to Rfam database...	0.61	0.50	0.74	65	74603	26	5	18	3	65
ASE_00257	RNaseP_bact_a links to Rfam database...	0.72	0.58	0.90	56	50978	9	4	2	3	41
ASE_00267	RNaseP_bact_a links to Rfam database...	0.75	0.65	0.86	57	45084	12	2	7	3	31
ASE_00270	RNaseP_bact_a links to Rfam database...	0.39	0.27	0.56	35	72328	32	0	27	5	93
ASE_00274	RNaseP_bact_a links to Rfam database...	0.60	0.48	0.77	49	55547	18	1	14	3	54
ASE_00277	RNaseP_bact_a links to Rfam database...	0.60	0.48	0.75	44	48146	19	1	14	4	47
ASE_00279	RNaseP_bact_a links to Rfam database...	0.78	0.65	0.93	66	53230	8	2	3	3	35
ASE_00285	RNaseP_bact_a links to Rfam database...	0.51	0.40	0.64	49	68930	30	2	25	3	73
ASE_00287	RNaseP_bact_a links to Rfam database...	0.67	0.54	0.84	56	54879	14	2	9	3	47
ASE_00294	RNaseP_bact_a links to Rfam database...	0.67	0.51	0.87	88	114380	16	2	11	3	83
ASE_00295	RNaseP_bact_a links to Rfam database...	0.76	0.63	0.92	82	73831	10	2	5	3	49
ASE_00298	RNaseP_bact_a links to Rfam database...	0.55	0.42	0.72	47	67463	21	4	14	3	66
ASE_00318	RNaseP_bact_b links to Rfam database...	0.63	0.54	0.74	64	80113	37	6	17	14	54
ASE_00321	RNaseP_bact_b links to Rfam database...	0.74	0.69	0.79	61	54538	25	4	12	9	27
ASE_00335	RNaseP_bact_b links to Rfam database...	0.72	0.66	0.78	76	75369	33	6	15	12	40
ASE_00339	RNaseP_bact_a links to Rfam database...	0.44	0.34	0.58	40	80131	37	3	26	8	79
ASE_00340	RNaseP_bact_a links to Rfam database...	0.51	0.45	0.59	38	45992	31	3	23	5	47
ASE_00343	RNaseP_bact_a links to Rfam database...	0.27	0.20	0.35	23	83371	49	4	38	7	90
ASE_00367	RNaseP_bact_a links to Rfam database...	0.79	0.71	0.88	61	43002	11	2	6	3	25
ASE_00370	RNaseP_bact_a links to Rfam database...	0.81	0.71	0.92	60	41840	8	1	4	3	24
ASE_00372	RNaseP_bact_a links to Rfam database...	0.57	0.45	0.71	45	51940	21	2	16	3	55
ASE_00375	RNaseP_bact_a links to Rfam database...	0.50	0.39	0.64	43	60311	26	1	23	2	67
ASE_00376	RNaseP_bact_a links to Rfam database...	0.65	0.55	0.76	58	56877	21	2	16	3	47
ASE_00377	RNaseP_bact_a links to Rfam database...	0.72	0.58	0.89	62	57560	11	1	7	3	45
ASE_00386	RNaseP_bact_a links to Rfam database...	0.75	0.61	0.92	59	50339	8	1	4	3	37
ASE_00393	RNaseP_bact_a links to Rfam database...	0.68	0.57	0.82	53	47830	15	1	11	3	40
ASE_00412	RNaseP_bact_a links to Rfam database...	0.55	0.42	0.72	44	58250	20	1	16	3	61
ASE_00413	RNaseP_bact_a links to Rfam database...	0.68	0.57	0.82	46	44495	14	1	9	4	35
ASE_00416	RNaseP_bact_a links to Rfam database...	0.69	0.60	0.80	76	77326	23	3	16	4	51
ASE_00417	RNaseP_arch links to Rfam database...	0.78	0.63	0.95	63	54549	5	0	3	2	37
ASE_00422	RNaseP_bact_a links to Rfam database...	0.58	0.49	0.69	46	46904	24	3	18	3	48
ASE_00427	RNaseP_nuc links to Rfam database...	0.56	0.41	0.76	19	40730	18	1	5	12	27
ASE_00428	RNaseP_bact_a links to Rfam database...	0.69	0.60	0.80	75	76542	22	5	14	3	50
ASE_00430	RNaseP_bact_a links to Rfam database...	0.55	0.45	0.68	44	46906	24	1	20	3	53
ASE_00434	RNaseP_bact_b links to Rfam database...	0.62	0.55	0.71	60	68180	34	5	20	9	50
ASE_00437	RNaseP_bact_a links to Rfam database...	0.58	0.50	0.69	67	79304	33	2	28	3	68
ASE_00451	RNaseP_bact_a links to Rfam database...	0.77	0.66	0.88	83	70782	14	2	9	3	42
ASE_00454	RNaseP_nuc links to Rfam database...	0.05	0.03	0.09	2	43342	25	1	20	4	61
CRW_00671	Intron_gpI links to Rfam database...	0.56	0.37	0.84	43	62784	10	0	8	2	74
CRW_00672	Intron_gpI links to Rfam database...	0.43	0.28	0.67	31	72344	17	0	15	2	80
CRW_00674	Intron_gpI links to Rfam database...	0.22	0.14	0.37	17	83390	29	5	24	0	107
CRW_00676	Intron_gpI links to Rfam database...	0.03	0.02	0.07	2	93500	31	4	22	5	113
CRW_01535	5S_rRNA links to Rfam database...	0.89	0.89	0.89	33	7103	8	0	4	4	4
CRW_01590	5S_rRNA links to Rfam database...	0.92	0.92	0.92	34	7103	7	0	3	4	3
CRW_01603	5S_rRNA links to Rfam database...	0.89	0.89	0.89	33	7103	8	0	4	4	4
PDB_00828	Purine links to Rfam database...	0.82	0.67	1.00	18	2467	0	0	0	0	9
PDB_01051	Telomerase-cil links to Rfam database...	0.64	0.54	0.78	7	894	5	0	2	3	6
PDB_01236	ykoK links to Rfam database...	0.87	0.81	0.94	44	11581	8	0	3	5	10
RFA_00416	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1471	1	0	0	1	1
RFA_00434	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	1	0	0	1	1
RFA_00436	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	1	0	0	1	1
RFA_00442	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	1	0	0	1	1
RFA_00446	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1471	1	0	0	1	1
RFA_00604	Telomerase-cil links to Rfam database...	0.72	0.63	0.81	22	13503	13	3	2	8	13
RFA_00620	Telomerase-cil links to Rfam database...	0.20	0.18	0.23	7	21915	33	7	16	10	32
RFA_00664	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	978	4	0	3	1	5
RFA_00674	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	1116	4	0	3	1	5
RFA_00675	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	978	4	0	3	1	5
RFA_00677	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	978	4	0	3	1	5
RFA_00684	Hammerhead_1 links to Rfam database...	0.66	0.64	0.69	9	977	5	0	4	1	5
RFA_00703	Hammerhead_1 links to Rfam database...	0.62	0.57	0.67	8	4266	8	1	3	4	6
RFA_00716	Hammerhead_1 links to Rfam database...	0.48	0.43	0.55	6	935	6	0	5	1	8
RFA_00717	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	891	3	0	3	0	5
RFA_00730	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00763	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00765	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00770	Corona_pk3 links to Rfam database...	0.57	0.56	0.59	10	1999	7	2	5	0	8
RFA_00773	Corona_pk3 links to Rfam database...	0.55	0.56	0.56	10	1935	8	3	5	0	8
RFA_00808	RydC links to Rfam database...	-0.01	0.00	0.00	0	2000	19	2	14	3	16
RFA_00816	R2_retro_el links to Rfam database...	0.96	0.93	1.00	38	23182	15	0	0	15	3
SPR_00314	tRNA links to Rfam database...	1.00	1.00	1.00	21	2905	0	0	0	0	0
SPR_00452	tRNA links to Rfam database...	0.98	0.95	1.00	20	2830	0	0	0	0	1
SRP_00038	Bacteria_small_SRP links to Rfam database...	0.73	0.70	0.77	23	5020	9	0	7	2	10
SRP_00046	Bacteria_small_SRP links to Rfam database...	0.95	0.94	0.97	30	4722	3	0	1	2	2
SRP_00103	Metazoa_SRP links to Rfam database...	0.91	0.89	0.92	91	45352	17	0	8	9	11
SRP_00117	Metazoa_SRP links to Rfam database...	0.81	0.78	0.83	80	45355	24	0	16	8	22
SRP_00144	Archaea_SRP links to Rfam database...	0.87	0.86	0.87	81	46572	28	0	12	16	13
SRP_00170	Bacteria_small_SRP links to Rfam database...	0.51	0.48	0.55	12	4073	14	1	9	4	13
SRP_00173	Bacteria_large_SRP links to Rfam database...	0.78	0.70	0.86	63	38153	15	0	10	5	27
SRP_00194	Bacteria_small_SRP links to Rfam database...	0.74	0.76	0.73	16	3218	9	0	6	3	5
SRP_00197	Archaea_SRP links to Rfam database...	0.92	0.90	0.94	91	49358	24	0	6	18	10
SRP_00198	Archaea_SRP links to Rfam database...	0.90	0.87	0.92	90	50942	24	0	8	16	13
SRP_00200	Bacteria_small_SRP links to Rfam database...	0.72	0.67	0.77	24	6872	10	1	6	3	12
SRP_00216	Bacteria_small_SRP links to Rfam database...	0.76	0.70	0.83	19	3380	6	1	3	2	8
SRP_00229	Bacteria_small_SRP links to Rfam database...	0.40	0.41	0.41	11	5226	20	0	16	4	16
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...	0.84	0.76	0.93	65	36245	14	0	5	9	21
SRP_00243	Bacteria_small_SRP links to Rfam database...	0.78	0.74	0.82	23	5123	6	0	5	1	8
SRP_00244	Bacteria_small_SRP links to Rfam database...	0.71	0.64	0.78	25	6871	10	1	6	3	14
SRP_00266	Bacteria_small_SRP links to Rfam database...	0.57	0.59	0.57	17	4626	14	2	11	1	12
SRP_00267	Metazoa_SRP links to Rfam database...	0.89	0.89	0.90	85	44457	21	0	9	12	11
SRP_00269	Bacteria_small_SRP links to Rfam database...	0.87	0.82	0.93	27	5021	3	0	2	1	6
SRP_00273	Bacteria_small_SRP links to Rfam database...	0.74	0.65	0.84	26	6755	8	1	4	3	14
SRP_00276	Archaea_SRP links to Rfam database...	0.93	0.91	0.94	100	50615	13	0	6	7	10
SRP_00278	Archaea_SRP links to Rfam database...	0.73	0.69	0.77	72	45963	26	0	21	5	33
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.86	0.80	0.92	24	3715	3	0	2	1	6
SRP_00303	Bacteria_small_SRP links to Rfam database...	0.71	0.69	0.73	22	6640	13	1	7	5	10
SRP_00308	Bacteria_large_SRP links to Rfam database...	0.82	0.73	0.91	64	36245	15	0	6	9	24
SRP_00317	Metazoa_SRP links to Rfam database...	0.89	0.87	0.92	85	45058	22	0	7	15	13
SRP_00321	Archaea_SRP links to Rfam database...	0.76	0.75	0.78	81	47482	30	0	23	7	27
SRP_00322	Archaea_SRP links to Rfam database...	0.79	0.75	0.83	82	48417	26	0	17	9	27
SRP_00332	Archaea_SRP links to Rfam database...	0.95	0.93	0.97	99	50301	15	0	3	12	7
SRP_00333	Bacteria_small_SRP links to Rfam database...	0.92	0.88	0.97	30	5120	2	0	1	1	4
SRP_00337	Bacteria_large_SRP links to Rfam database...	0.78	0.71	0.84	65	35434	14	1	11	2	26
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.75	0.72	0.79	26	5427	8	0	7	1	10
SRP_00342	Bacteria_small_SRP links to Rfam database...	0.71	0.68	0.74	17	3982	8	1	5	2	8
SRP_00358	Bacteria_small_SRP links to Rfam database...	0.83	0.77	0.90	27	6298	6	1	2	3	8
SRP_00383	Bacteria_small_SRP links to Rfam database...	0.75	0.67	0.84	16	3221	5	0	3	2	8
TMR_00357	tmRNA links to Rfam database...	0.19	0.13	0.28	12	82985	38	4	27	7	80

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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	2117
Total TN	4584648
Total FP	10017
Total FP CONTRA	1492
Total FP INCONS	8245
Total FP COMP	280
Total FN	7001

Total Scores
MCC	0.202
Average MCC ± 95% Confidence Intervals	0.260 ± 0.038
Sensitivity	0.232
Positive Predictive Value	0.179
Nr of predictions	126

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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_00017	RNaseP_nuc links to Rfam database...	0.02	0.03	0.02	2	50914	131	38	86	7	62
ASE_00083	RNaseP_bact_a links to Rfam database...	0.22	0.25	0.20	27	62347	108	12	95	1	83
ASE_00122	RNaseP_bact_a links to Rfam database...	0.27	0.30	0.24	26	43258	84	13	68	3	62
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_00191	RNaseP_arch links to Rfam database...	0.36	0.43	0.30	26	29559	67	15	46	6	35
ASE_00196	RNaseP_arch links to Rfam database...	0.49	0.57	0.42	43	31524	62	16	43	3	32
ASE_00221	RNaseP_bact_a links to Rfam database...	0.20	0.21	0.18	25	64484	112	10	101	1	92
ASE_00227	RNaseP_bact_a links to Rfam database...	0.28	0.31	0.25	41	78840	122	20	102	0	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_00250	RNaseP_bact_a links to Rfam database...	0.25	0.29	0.23	38	78835	135	17	113	5	93
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_00295	RNaseP_bact_a links to Rfam database...	0.14	0.16	0.13	21	73761	140	19	119	2	110
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_00339	RNaseP_bact_a links to Rfam database...	0.25	0.29	0.22	34	80042	129	20	104	5	85
ASE_00340	RNaseP_bact_a links to Rfam database...	0.06	0.07	0.05	6	45943	110	13	94	3	79
ASE_00343	RNaseP_bact_a links to Rfam database...	0.14	0.17	0.12	19	83275	145	31	111	3	94
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_00375	RNaseP_bact_a links to Rfam database...	0.12	0.14	0.11	15	60246	120	10	107	3	95
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_00417	RNaseP_arch links to Rfam database...	0.32	0.36	0.28	36	54486	98	18	75	5	64
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_00434	RNaseP_bact_b links to Rfam database...	0.29	0.34	0.25	37	68116	122	20	92	10	73
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
ASE_00454	RNaseP_nuc links to Rfam database...	0.24	0.32	0.19	20	43260	103	28	57	18	43
CRW_00671	Intron_gpI links to Rfam database...	0.18	0.21	0.16	24	62682	130	23	106	1	93
CRW_00672	Intron_gpI links to Rfam database...	0.36	0.43	0.31	48	72233	114	35	74	5	63
CRW_00674	Intron_gpI links to Rfam database...	0.16	0.19	0.14	23	83274	142	19	120	3	101
CRW_00676	Intron_gpI links to Rfam database...	0.11	0.14	0.09	16	93347	169	29	136	4	99
CRW_01535	5S_rRNA links to Rfam database...	0.20	0.24	0.17	9	7088	43	7	36	0	28
CRW_01590	5S_rRNA links to Rfam database...	-0.01	0.00	0.00	0	7093	50	7	40	3	37
CRW_01603	5S_rRNA links to Rfam database...	0.41	0.46	0.38	17	7095	29	6	22	1	20
PDB_00828	Purine links to Rfam database...	0.30	0.33	0.28	9	2453	23	0	23	0	18
PDB_01051	Telomerase-cil links to Rfam database...	-0.02	0.00	0.00	0	885	18	1	17	0	13
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_00446	Hammerhead_3 links to Rfam database...	0.85	0.93	0.78	14	1467	7	3	1	3	1
RFA_00604	Telomerase-cil links to Rfam database...	0.42	0.54	0.33	19	13472	53	14	25	14	16
RFA_00620	Telomerase-cil links to Rfam database...	0.16	0.23	0.11	9	21864	80	29	43	8	30
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_00684	Hammerhead_1 links to Rfam database...	0.74	0.71	0.77	10	977	5	2	1	2	4
RFA_00703	Hammerhead_1 links to Rfam database...	0.26	0.36	0.19	5	4252	32	5	16	11	9
RFA_00716	Hammerhead_1 links to Rfam database...	-0.02	0.00	0.00	0	929	17	0	17	0	14
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
RFA_00770	Corona_pk3 links to Rfam database...	-0.01	0.00	0.00	0	1996	24	0	20	4	18
RFA_00773	Corona_pk3 links to Rfam database...	0.93	1.00	0.86	18	1932	9	3	0	6	0
RFA_00808	RydC links to Rfam database...	0.83	1.00	0.70	16	1993	7	7	0	0	0
RFA_00816	R2_retro_el links to Rfam database...	0.00	0.00	0.00	0	23133	89	30	57	2	41
SPR_00314	tRNA links to Rfam database...	0.47	0.57	0.39	12	2895	21	9	10	2	9
SPR_00452	tRNA links to Rfam database...	0.27	0.33	0.23	7	2820	24	7	16	1	14
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_00117	Metazoa_SRP links to Rfam database...	0.20	0.23	0.18	23	45322	106	9	97	0	79
SRP_00144	Archaea_SRP links to Rfam database...	0.05	0.06	0.05	6	46538	122	17	104	1	88
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_00197	Archaea_SRP links to Rfam database...	0.12	0.14	0.11	14	49324	117	16	101	0	87
SRP_00198	Archaea_SRP links to Rfam database...	0.07	0.08	0.06	8	50903	129	15	114	0	95
SRP_00200	Bacteria_small_SRP links to Rfam database...	0.41	0.47	0.35	17	6855	31	4	27	0	19
SRP_00216	Bacteria_small_SRP links to Rfam database...	0.44	0.48	0.41	13	3371	19	4	15	0	14
SRP_00229	Bacteria_small_SRP links to Rfam database...	0.42	0.52	0.35	14	5213	26	8	18	0	13
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_00243	Bacteria_small_SRP links to Rfam database...	0.47	0.55	0.40	17	5109	25	7	18	0	14
SRP_00244	Bacteria_small_SRP links to Rfam database...	0.38	0.44	0.34	17	6853	33	2	31	0	22
SRP_00266	Bacteria_small_SRP links to Rfam database...	0.55	0.66	0.46	19	4615	22	8	14	0	10
SRP_00267	Metazoa_SRP links to Rfam database...	0.04	0.05	0.04	5	44424	122	15	107	0	91
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_00276	Archaea_SRP links to Rfam database...	0.19	0.22	0.18	24	50585	112	10	102	0	86
SRP_00278	Archaea_SRP links to Rfam database...	0.33	0.36	0.30	38	45928	90	14	76	0	67
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.38	0.43	0.35	13	3704	24	6	18	0	17
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_00321	Archaea_SRP links to Rfam database...	0.44	0.49	0.40	53	47453	81	16	64	1	55
SRP_00322	Archaea_SRP links to Rfam database...	0.22	0.25	0.21	27	48385	105	8	96	1	82
SRP_00332	Archaea_SRP links to Rfam database...	0.12	0.14	0.11	15	50269	120	8	111	1	91
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_00357	tmRNA links to Rfam database...	0.26	0.34	0.19	31	82869	146	44	84	18	61

^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 MXScarna(seed) - scored higher in this pairwise comparison

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

2. Individual counts for MXScarna(seed) [ 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 ]