CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	Murlet(20)		PknotsRG
MCC	0.586	>	0.486
Average MCC ± 95% Confidence Intervals	0.563 ± 0.021	>	0.491 ± 0.026
Sensitivity	0.458	<	0.479
Positive Predictive Value	0.751	>	0.494
Total TP	8294	<	8675
Total TN	16205123	>	16198604
Total FP	3140	<	9709
Total FP CONTRA	397	<	1246
Total FP INCONS	2351	<	7640
Total FP COMP	392	<	823
Total FN	9810	>	9429
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of Murlet(20) and PknotsRG. 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 Murlet(20) and PknotsRG).
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 Murlet(20) and PknotsRG).
Comparison of average Matthews Correlation Coefficients (MCCs) for Murlet(20) and PknotsRG. 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 Murlet(20) and PknotsRG).

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

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

Total Base Pair Counts
Total TP	8294
Total TN	16205123
Total FP	3140
Total FP CONTRA	397
Total FP INCONS	2351
Total FP COMP	392
Total FN	9810

Total Scores
MCC	0.586
Average MCC ± 95% Confidence Intervals	0.563 ± 0.021
Sensitivity	0.458
Positive Predictive Value	0.751
Nr of predictions	156

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
ASE_00004	RNaseP_bact_a links to Rfam database...	0.46	0.34	0.61	33	47841	21	1	20	0	64
ASE_00007	RNaseP_bact_a links to Rfam database...	0.71	0.57	0.89	63	59614	8	2	6	0	47
ASE_00018	RNaseP_bact_a links to Rfam database...	0.61	0.45	0.82	60	80528	13	3	10	0	74
ASE_00022	RNaseP_bact_b links to Rfam database...	0.67	0.50	0.89	62	82958	15	0	8	7	62
ASE_00028	RNaseP_bact_b links to Rfam database...	0.56	0.40	0.77	51	84600	15	5	10	0	75
ASE_00035	RNaseP_bact_a links to Rfam database...	0.62	0.49	0.79	58	70427	17	4	11	2	60
ASE_00040	RNaseP_bact_a links to Rfam database...	0.62	0.43	0.90	57	78940	6	0	6	0	76
ASE_00064	RNaseP_bact_a links to Rfam database...	0.55	0.39	0.76	35	45405	14	3	8	3	54
ASE_00068	RNaseP_bact_a links to Rfam database...	0.62	0.42	0.90	36	37635	4	3	1	0	49
ASE_00075	RNaseP_bact_a links to Rfam database...	0.51	0.34	0.76	55	108739	19	1	16	2	107
ASE_00077	RNaseP_bact_a links to Rfam database...	0.48	0.35	0.67	30	45105	18	0	15	3	56
ASE_00078	RNaseP_bact_a links to Rfam database...	0.64	0.53	0.79	44	43015	12	3	9	0	39
ASE_00080	RNaseP_bact_a links to Rfam database...	0.31	0.21	0.46	26	71574	31	3	28	0	97
ASE_00081	RNaseP_bact_a links to Rfam database...	0.73	0.58	0.93	56	49710	5	0	4	1	41
ASE_00082	RNaseP_bact_a links to Rfam database...	0.27	0.20	0.37	23	70438	42	2	37	3	93
ASE_00083	RNaseP_bact_a links to Rfam database...	0.54	0.39	0.75	43	62424	14	2	12	0	67
ASE_00084	RNaseP_bact_a links to Rfam database...	0.53	0.36	0.77	36	53581	12	0	11	1	63
ASE_00087	RNaseP_bact_a links to Rfam database...	0.35	0.21	0.58	30	88358	22	0	22	0	114
ASE_00092	RNaseP_bact_a links to Rfam database...	0.58	0.40	0.85	45	63493	10	0	8	2	68
ASE_00104	RNaseP_bact_a links to Rfam database...	0.51	0.38	0.69	45	64196	20	1	19	0	74
ASE_00107	RNaseP_bact_a links to Rfam database...	0.64	0.48	0.86	61	73082	13	2	8	3	66
ASE_00115	RNaseP_bact_a links to Rfam database...	0.46	0.30	0.71	30	54573	12	1	11	0	71
ASE_00119	RNaseP_bact_a links to Rfam database...	0.11	0.08	0.16	9	62779	48	2	45	1	99
ASE_00123	RNaseP_bact_a links to Rfam database...	0.55	0.40	0.76	34	38458	11	0	11	0	51
ASE_00135	RNaseP_bact_a links to Rfam database...	0.34	0.24	0.49	26	63137	29	3	24	2	83
ASE_00138	RNaseP_bact_a links to Rfam database...	0.60	0.47	0.76	38	40420	13	0	12	1	43
ASE_00142	RNaseP_bact_a links to Rfam database...	0.52	0.40	0.68	49	67089	23	1	22	0	73
ASE_00146	RNaseP_bact_a links to Rfam database...	0.70	0.56	0.87	69	70797	13	0	10	3	55
ASE_00153	RNaseP_nuc links to Rfam database...	0.34	0.23	0.50	17	57596	26	3	14	9	56
ASE_00163	RNaseP_bact_a links to Rfam database...	0.47	0.32	0.70	30	53258	13	0	13	0	63
ASE_00170	RNaseP_bact_a links to Rfam database...	0.52	0.37	0.74	34	48782	12	0	12	0	59
ASE_00174	RNaseP_bact_a links to Rfam database...	0.30	0.23	0.39	25	61011	43	2	37	4	84
ASE_00179	RNaseP_bact_a links to Rfam database...	0.49	0.40	0.61	34	44197	22	0	22	0	50
ASE_00180	RNaseP_bact_a links to Rfam database...	0.70	0.55	0.90	55	51299	6	2	4	0	45
ASE_00182	RNaseP_bact_a links to Rfam database...	0.24	0.15	0.41	20	84206	31	1	28	2	116
ASE_00184	RNaseP_bact_a links to Rfam database...	0.58	0.42	0.80	43	54561	11	2	9	0	59
ASE_00185	RNaseP_bact_a links to Rfam database...	0.28	0.16	0.48	21	73492	23	0	23	0	107
ASE_00186	RNaseP_bact_a links to Rfam database...	0.61	0.45	0.84	59	78933	11	1	10	0	73
ASE_00190	RNaseP_bact_b links to Rfam database...	0.38	0.22	0.67	20	45421	12	0	10	2	70
ASE_00212	RNaseP_bact_a links to Rfam database...	0.55	0.39	0.78	58	93887	16	1	15	0	90
ASE_00214	RNaseP_bact_a links to Rfam database...	0.40	0.27	0.58	28	56232	21	1	19	1	75
ASE_00215	RNaseP_bact_a links to Rfam database...	0.46	0.31	0.69	31	48471	14	4	10	0	68
ASE_00217	RNaseP_bact_a links to Rfam database...	0.66	0.50	0.87	45	40418	7	1	6	0	45
ASE_00221	RNaseP_bact_a links to Rfam database...	0.58	0.44	0.78	51	64555	14	0	14	0	66
ASE_00228	RNaseP_bact_a links to Rfam database...	0.53	0.44	0.63	38	46911	23	1	21	1	48
ASE_00229	RNaseP_bact_a links to Rfam database...	0.61	0.48	0.76	42	42431	13	3	10	0	45
ASE_00238	RNaseP_bact_a links to Rfam database...	0.45	0.30	0.68	34	64211	16	2	14	0	80
ASE_00241	RNaseP_bact_a links to Rfam database...	0.66	0.55	0.79	48	43895	16	2	11	3	39
ASE_00248	RNaseP_bact_a links to Rfam database...	0.76	0.63	0.91	72	62402	7	0	7	0	42
ASE_00255	RNaseP_bact_a links to Rfam database...	0.53	0.39	0.72	51	74620	21	1	19	1	79
ASE_00257	RNaseP_bact_a links to Rfam database...	0.55	0.43	0.69	42	50979	19	0	19	0	55
ASE_00267	RNaseP_bact_a links to Rfam database...	0.76	0.61	0.95	54	45093	4	2	1	1	34
ASE_00270	RNaseP_bact_a links to Rfam database...	0.21	0.14	0.32	18	72333	41	0	39	2	110
ASE_00279	RNaseP_bact_a links to Rfam database...	0.63	0.48	0.84	48	53244	9	1	8	0	53
ASE_00280	RNaseP_bact_a links to Rfam database...	0.67	0.54	0.84	53	51940	10	3	7	0	45
ASE_00281	RNaseP_bact_a links to Rfam database...	0.74	0.60	0.91	53	44493	5	0	5	0	35
ASE_00283	RNaseP_bact_a links to Rfam database...	0.55	0.41	0.73	44	61716	16	0	16	0	63
ASE_00285	RNaseP_bact_a links to Rfam database...	0.45	0.33	0.62	40	68941	25	1	24	0	82
ASE_00292	RNaseP_bact_a links to Rfam database...	0.52	0.36	0.74	50	81742	18	1	17	0	88
ASE_00294	RNaseP_bact_a links to Rfam database...	0.55	0.37	0.83	63	114405	14	4	9	1	108
ASE_00297	RNaseP_bact_a links to Rfam database...	0.59	0.41	0.85	40	52928	10	0	7	3	58
ASE_00298	RNaseP_bact_a links to Rfam database...	0.22	0.15	0.32	17	67475	36	4	32	0	96
ASE_00318	RNaseP_bact_b links to Rfam database...	0.66	0.49	0.89	58	80135	16	2	5	9	60
ASE_00328	RNaseP_bact_b links to Rfam database...	0.59	0.48	0.72	54	72696	27	5	16	6	58
ASE_00332	RNaseP_bact_a links to Rfam database...	0.63	0.47	0.83	65	81732	13	2	11	0	73
ASE_00335	RNaseP_bact_b links to Rfam database...	0.60	0.48	0.76	56	75392	19	5	13	1	60
ASE_00340	RNaseP_bact_a links to Rfam database...	0.45	0.34	0.60	29	46008	22	3	16	3	56
ASE_00353	RNaseP_bact_a links to Rfam database...	0.50	0.35	0.71	37	57918	15	0	15	0	70
ASE_00361	RNaseP_bact_a links to Rfam database...	0.57	0.39	0.82	50	75405	11	1	10	0	77
ASE_00362	RNaseP_bact_a links to Rfam database...	0.56	0.38	0.81	35	48162	12	0	8	4	56
ASE_00363	RNaseP_bact_a links to Rfam database...	0.61	0.44	0.85	41	51312	7	0	7	0	53
ASE_00364	RNaseP_bact_a links to Rfam database...	0.58	0.38	0.89	40	54240	5	0	5	0	65
ASE_00366	RNaseP_bact_a links to Rfam database...	0.49	0.36	0.67	35	58601	19	0	17	2	63
ASE_00367	RNaseP_bact_a links to Rfam database...	0.71	0.57	0.89	49	43016	6	2	4	0	37
ASE_00372	RNaseP_bact_a links to Rfam database...	0.40	0.31	0.53	31	51944	28	3	25	0	69
ASE_00376	RNaseP_bact_a links to Rfam database...	0.57	0.40	0.82	42	56902	9	2	7	0	63
ASE_00382	RNaseP_bact_a links to Rfam database...	0.65	0.51	0.83	43	41853	9	2	7	0	41
ASE_00384	RNaseP_bact_a links to Rfam database...	0.59	0.43	0.80	40	48466	10	2	8	0	52
ASE_00386	RNaseP_bact_a links to Rfam database...	0.54	0.36	0.80	35	50359	9	1	8	0	61
ASE_00387	RNaseP_bact_a links to Rfam database...	0.64	0.45	0.90	47	55893	5	0	5	0	57
ASE_00388	RNaseP_bact_a links to Rfam database...	0.53	0.38	0.72	34	45706	16	1	12	3	55
ASE_00390	RNaseP_bact_a links to Rfam database...	0.77	0.64	0.93	54	42137	6	1	3	2	31
ASE_00393	RNaseP_bact_a links to Rfam database...	0.55	0.41	0.73	38	47843	15	3	11	1	55
ASE_00394	RNaseP_bact_a links to Rfam database...	0.56	0.41	0.78	38	46922	11	1	10	0	55
ASE_00395	RNaseP_bact_a links to Rfam database...	0.68	0.51	0.90	43	41568	5	0	5	0	41
ASE_00396	RNaseP_bact_a links to Rfam database...	0.62	0.47	0.81	39	41568	9	0	9	0	44
ASE_00397	RNaseP_bact_a links to Rfam database...	0.63	0.45	0.89	47	54562	9	1	5	3	58
ASE_00398	RNaseP_bact_a links to Rfam database...	0.49	0.32	0.75	33	55901	12	0	11	1	71
ASE_00400	RNaseP_bact_a links to Rfam database...	0.47	0.36	0.61	38	57908	25	3	21	1	68
ASE_00402	RNaseP_bact_a links to Rfam database...	0.55	0.35	0.86	30	42451	5	2	3	0	55
ASE_00404	RNaseP_bact_a links to Rfam database...	0.72	0.55	0.94	47	43021	4	0	3	1	38
ASE_00406	RNaseP_bact_a links to Rfam database...	0.60	0.44	0.84	41	48779	8	0	8	0	53
ASE_00411	RNaseP_bact_a links to Rfam database...	0.59	0.39	0.88	35	49415	5	0	5	0	54
ASE_00412	RNaseP_bact_a links to Rfam database...	0.51	0.32	0.79	34	58268	11	0	9	2	71
ASE_00416	RNaseP_bact_a links to Rfam database...	0.45	0.33	0.62	42	77353	26	1	25	0	85
ASE_00419	RNaseP_bact_a links to Rfam database...	0.49	0.33	0.74	34	54900	12	2	10	0	69
ASE_00422	RNaseP_bact_a links to Rfam database...	0.50	0.35	0.70	33	46924	14	0	14	0	61
ASE_00423	RNaseP_bact_a links to Rfam database...	0.65	0.53	0.79	58	56880	15	0	15	0	51
ASE_00428	RNaseP_bact_a links to Rfam database...	0.47	0.34	0.67	42	76573	21	4	17	0	83
ASE_00430	RNaseP_bact_a links to Rfam database...	0.50	0.37	0.68	36	46918	17	0	17	0	61
ASE_00437	RNaseP_bact_a links to Rfam database...	0.42	0.32	0.56	43	79324	34	3	31	0	92
ASE_00448	RNaseP_bact_a links to Rfam database...	0.63	0.49	0.82	55	64194	12	3	9	0	57
ASE_00451	RNaseP_bact_a links to Rfam database...	0.56	0.41	0.76	51	70809	16	1	15	0	74
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.75	0.70	0.81	330	1178473	93	14	63	16	143
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.75	0.68	0.84	325	1198537	73	14	50	9	153
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.75	0.67	0.83	302	1129893	75	12	49	14	148
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.78	0.72	0.85	328	1117874	75	11	47	17	125
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.78	0.71	0.86	318	1137416	79	8	44	27	129
PDB_00571	tRNA links to Rfam database...	0.59	0.52	0.68	13	3302	7	0	6	1	12
PDB_00828	Purine links to Rfam database...	0.84	0.70	1.00	19	2466	0	0	0	0	8
PDB_00829	Purine links to Rfam database...	0.82	0.67	1.00	16	2262	0	0	0	0	8
PDB_01020	Purine links to Rfam database...	0.83	0.70	1.00	16	2262	0	0	0	0	7
PDB_01073	SAM links to Rfam database...	0.66	0.44	1.00	15	4356	1	0	0	1	19
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.73	0.62	0.86	337	1433581	81	3	50	28	203
RFA_00599	Telomerase-vert links to Rfam database...	0.44	0.34	0.58	38	101409	33	1	27	5	73
RFA_00601	Telomerase-vert links to Rfam database...	0.31	0.23	0.42	26	99173	43	3	33	7	88
RFA_00602	Telomerase-vert links to Rfam database...	0.24	0.16	0.35	19	101421	41	2	33	6	97
TMR_00017	tmRNA links to Rfam database...	0.72	0.60	0.87	61	67091	13	0	9	4	41
TMR_00018	tmRNA links to Rfam database...	0.56	0.49	0.65	45	64551	29	6	18	5	47
TMR_00038	tmRNA links to Rfam database...	0.67	0.53	0.84	58	71184	13	5	6	2	52
TMR_00042	tmRNA links to Rfam database...	0.56	0.44	0.70	43	62774	19	1	17	1	55
TMR_00046	tmRNA links to Rfam database...	0.60	0.52	0.69	50	62763	23	6	16	1	46
TMR_00048	tmRNA links to Rfam database...	0.56	0.48	0.66	46	64910	29	9	15	5	49
TMR_00080	tmRNA links to Rfam database...	0.54	0.49	0.60	47	70422	35	12	19	4	49
TMR_00082	tmRNA links to Rfam database...	0.59	0.50	0.71	48	67828	25	7	13	5	48
TMR_00123	tmRNA links to Rfam database...	0.64	0.50	0.81	51	66367	17	3	9	5	50
TMR_00137	tmRNA links to Rfam database...	0.54	0.46	0.64	41	61011	28	5	18	5	48
TMR_00142	tmRNA links to Rfam database...	0.64	0.60	0.69	61	70788	34	12	15	7	41
TMR_00207	tmRNA links to Rfam database...	0.53	0.42	0.66	43	72325	26	4	18	4	60
TMR_00257	tmRNA links to Rfam database...	0.56	0.48	0.64	47	67088	29	4	22	3	51
TMR_00271	tmRNA links to Rfam database...	0.55	0.42	0.72	38	64208	20	1	14	5	53
TMR_00332	tmRNA links to Rfam database...	0.70	0.58	0.85	57	67094	16	0	10	6	42
TMR_00366	tmRNA links to Rfam database...	0.53	0.49	0.58	49	67811	43	8	28	7	51
TMR_00378	tmRNA links to Rfam database...	0.57	0.51	0.64	49	67820	37	9	18	10	48
TMR_00399	tmRNA links to Rfam database...	0.61	0.47	0.79	44	64924	18	2	10	6	50
TMR_00404	tmRNA links to Rfam database...	0.53	0.41	0.68	38	67472	21	8	10	3	54
TMR_00427	tmRNA links to Rfam database...	0.20	0.13	0.30	13	67485	30	4	26	0	84
TMR_00443	tmRNA links to Rfam database...	0.73	0.61	0.88	63	67089	13	0	9	4	41
TMR_00451	tmRNA links to Rfam database...	0.52	0.46	0.58	41	63475	36	8	22	6	48
TMR_00458	tmRNA links to Rfam database...	0.50	0.41	0.61	38	63484	29	4	20	5	55
TMR_00469	tmRNA links to Rfam database...	0.64	0.48	0.84	48	64563	10	3	6	1	52
TMR_00472	tmRNA links to Rfam database...	0.70	0.61	0.81	59	64547	15	8	6	1	38
TMR_00519	tmRNA links to Rfam database...	0.49	0.37	0.65	35	63136	23	2	17	4	60
TMR_00520	tmRNA links to Rfam database...	0.44	0.35	0.54	35	63125	36	5	25	6	64
TMR_00522	tmRNA links to Rfam database...	0.49	0.39	0.60	38	63127	29	8	17	4	59
TMR_00528	tmRNA links to Rfam database...	0.48	0.41	0.57	40	63120	36	7	23	6	57
TMR_00540	tmRNA links to Rfam database...	0.53	0.45	0.63	47	73461	28	8	20	0	57
TMR_00568	tmRNA links to Rfam database...	0.72	0.64	0.82	63	60649	18	3	11	4	36
TMR_00571	tmRNA links to Rfam database...	0.76	0.67	0.86	66	60649	15	2	9	4	33
TMR_00580	tmRNA links to Rfam database...	0.75	0.66	0.86	66	60649	15	2	9	4	34
TMR_00584	tmRNA links to Rfam database...	0.71	0.62	0.81	60	61001	17	4	10	3	37
TMR_00586	tmRNA links to Rfam database...	0.71	0.63	0.79	61	60998	20	5	11	4	36
TMR_00616	tmRNA links to Rfam database...	0.67	0.58	0.79	57	67089	16	6	9	1	42
TMR_00699	tmRNA links to Rfam database...	0.57	0.43	0.75	44	67102	19	1	14	4	58
TMR_00702	tmRNA links to Rfam database...	0.54	0.43	0.68	43	67098	25	3	17	5	57
TMR_00703	tmRNA links to Rfam database...	0.58	0.45	0.75	45	67468	19	3	12	4	54

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Performance of PknotsRG - scored lower in this pairwise comparison

1. Total counts & total scores for PknotsRG

Total Base Pair Counts
Total TP	8675
Total TN	16198604
Total FP	9709
Total FP CONTRA	1246
Total FP INCONS	7640
Total FP COMP	823
Total FN	9429

Total Scores
MCC	0.486
Average MCC ± 95% Confidence Intervals	0.491 ± 0.026
Sensitivity	0.479
Positive Predictive Value	0.494
Nr of predictions	156

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
ASE_00004	RNaseP_bact_a links to Rfam database...	0.70	0.71	0.70	69	47796	32	9	21	2	28
ASE_00007	RNaseP_bact_a links to Rfam database...	0.57	0.55	0.61	60	59586	43	1	38	4	50
ASE_00018	RNaseP_bact_a links to Rfam database...	0.80	0.76	0.84	102	80479	22	3	17	2	32
ASE_00022	RNaseP_bact_b links to Rfam database...	0.46	0.44	0.48	54	82915	65	6	53	6	70
ASE_00028	RNaseP_bact_b links to Rfam database...	0.59	0.56	0.61	71	84550	53	4	41	8	55
ASE_00035	RNaseP_bact_a links to Rfam database...	0.30	0.28	0.32	33	70398	76	11	58	7	85
ASE_00040	RNaseP_bact_a links to Rfam database...	0.50	0.47	0.52	63	78882	64	5	53	6	70
ASE_00064	RNaseP_bact_a links to Rfam database...	0.43	0.43	0.44	38	45364	53	5	44	4	51
ASE_00068	RNaseP_bact_a links to Rfam database...	0.24	0.24	0.25	20	37596	59	5	54	0	65
ASE_00075	RNaseP_bact_a links to Rfam database...	0.65	0.59	0.71	96	108676	46	2	37	7	66
ASE_00077	RNaseP_bact_a links to Rfam database...	0.25	0.24	0.25	21	45067	67	7	55	5	65
ASE_00078	RNaseP_bact_a links to Rfam database...	0.68	0.67	0.68	56	42989	31	5	21	5	27
ASE_00080	RNaseP_bact_a links to Rfam database...	0.46	0.44	0.48	54	71519	61	5	53	3	69
ASE_00081	RNaseP_bact_a links to Rfam database...	0.53	0.53	0.54	51	49676	44	5	38	1	46
ASE_00082	RNaseP_bact_a links to Rfam database...	0.50	0.47	0.54	54	70400	60	1	45	14	62
ASE_00083	RNaseP_bact_a links to Rfam database...	0.79	0.75	0.83	82	62382	26	2	15	9	28
ASE_00084	RNaseP_bact_a links to Rfam database...	0.70	0.69	0.72	68	53534	29	6	20	3	31
ASE_00087	RNaseP_bact_a links to Rfam database...	0.61	0.58	0.65	83	88283	49	5	39	5	61
ASE_00092	RNaseP_bact_a links to Rfam database...	0.73	0.70	0.76	79	63442	30	0	25	5	34
ASE_00104	RNaseP_bact_a links to Rfam database...	0.65	0.63	0.68	75	64151	36	3	32	1	44
ASE_00107	RNaseP_bact_a links to Rfam database...	0.47	0.45	0.50	57	73039	57	2	55	0	70
ASE_00115	RNaseP_bact_a links to Rfam database...	0.48	0.47	0.49	47	54520	56	1	47	8	54
ASE_00119	RNaseP_bact_a links to Rfam database...	0.67	0.65	0.69	70	62734	33	1	30	2	38
ASE_00123	RNaseP_bact_a links to Rfam database...	0.40	0.39	0.42	33	38424	50	2	44	4	52
ASE_00135	RNaseP_bact_a links to Rfam database...	0.47	0.46	0.48	50	63085	59	8	47	4	59
ASE_00138	RNaseP_bact_a links to Rfam database...	0.53	0.52	0.55	42	40393	35	4	31	0	39
ASE_00142	RNaseP_bact_a links to Rfam database...	0.74	0.70	0.79	85	67054	26	4	18	4	37
ASE_00146	RNaseP_bact_a links to Rfam database...	0.51	0.46	0.56	57	70775	47	0	44	3	67
ASE_00153	RNaseP_nuc links to Rfam database...	0.61	0.62	0.61	45	57556	71	2	27	42	28
ASE_00163	RNaseP_bact_a links to Rfam database...	0.29	0.29	0.30	27	53211	72	7	56	9	66
ASE_00170	RNaseP_bact_a links to Rfam database...	0.70	0.68	0.72	63	48741	25	2	22	1	30
ASE_00174	RNaseP_bact_a links to Rfam database...	0.55	0.51	0.59	56	60980	39	3	36	0	53
ASE_00179	RNaseP_bact_a links to Rfam database...	0.64	0.65	0.62	55	44164	34	7	27	0	29
ASE_00180	RNaseP_bact_a links to Rfam database...	0.72	0.69	0.75	69	51268	29	2	21	6	31
ASE_00182	RNaseP_bact_a links to Rfam database...	0.49	0.47	0.51	64	84129	65	6	56	3	72
ASE_00184	RNaseP_bact_a links to Rfam database...	0.63	0.64	0.63	65	54511	39	10	29	0	37
ASE_00185	RNaseP_bact_a links to Rfam database...	0.61	0.59	0.65	75	73420	43	5	36	2	53
ASE_00186	RNaseP_bact_a links to Rfam database...	0.74	0.70	0.78	92	78885	31	3	23	5	40
ASE_00190	RNaseP_bact_b links to Rfam database...	0.46	0.44	0.47	40	45366	45	8	37	0	50
ASE_00212	RNaseP_bact_a links to Rfam database...	0.54	0.52	0.55	77	93822	66	5	57	4	71
ASE_00214	RNaseP_bact_a links to Rfam database...	0.78	0.76	0.80	78	56182	28	3	17	8	25
ASE_00215	RNaseP_bact_a links to Rfam database...	0.55	0.53	0.57	52	48425	42	4	35	3	47
ASE_00217	RNaseP_bact_a links to Rfam database...	0.30	0.29	0.32	26	40388	60	6	50	4	64
ASE_00221	RNaseP_bact_a links to Rfam database...	0.40	0.38	0.42	45	64514	65	3	58	4	72
ASE_00228	RNaseP_bact_a links to Rfam database...	0.59	0.59	0.58	51	46883	37	14	23	0	35
ASE_00229	RNaseP_bact_a links to Rfam database...	0.58	0.57	0.59	50	42401	39	5	30	4	37
ASE_00238	RNaseP_bact_a links to Rfam database...	0.48	0.47	0.50	54	64152	58	4	51	3	60
ASE_00241	RNaseP_bact_a links to Rfam database...	0.56	0.54	0.58	47	43875	43	0	34	9	40
ASE_00248	RNaseP_bact_a links to Rfam database...	0.46	0.42	0.49	48	62384	49	3	46	0	66
ASE_00255	RNaseP_bact_a links to Rfam database...	0.47	0.45	0.50	59	74572	60	7	53	0	71
ASE_00257	RNaseP_bact_a links to Rfam database...	0.64	0.64	0.65	62	50944	34	0	34	0	35
ASE_00267	RNaseP_bact_a links to Rfam database...	0.46	0.44	0.48	39	45069	51	5	37	9	49
ASE_00270	RNaseP_bact_a links to Rfam database...	0.63	0.62	0.64	79	72267	45	8	36	1	49
ASE_00279	RNaseP_bact_a links to Rfam database...	0.38	0.36	0.41	36	53213	58	1	51	6	65
ASE_00280	RNaseP_bact_a links to Rfam database...	0.37	0.37	0.38	36	51908	62	6	53	3	62
ASE_00281	RNaseP_bact_a links to Rfam database...	0.54	0.51	0.58	45	44473	39	0	33	6	43
ASE_00283	RNaseP_bact_a links to Rfam database...	0.74	0.73	0.76	78	61673	27	5	20	2	29
ASE_00285	RNaseP_bact_a links to Rfam database...	0.62	0.58	0.66	71	68899	43	2	34	7	51
ASE_00292	RNaseP_bact_a links to Rfam database...	0.71	0.66	0.76	91	81690	34	4	25	5	47
ASE_00294	RNaseP_bact_a links to Rfam database...	0.78	0.74	0.83	127	114328	29	3	23	3	44
ASE_00297	RNaseP_bact_a links to Rfam database...	0.53	0.53	0.54	52	52878	50	3	42	5	46
ASE_00298	RNaseP_bact_a links to Rfam database...	0.19	0.19	0.19	21	67420	90	9	78	3	92
ASE_00318	RNaseP_bact_b links to Rfam database...	0.64	0.61	0.67	72	80092	40	13	23	4	46
ASE_00328	RNaseP_bact_b links to Rfam database...	0.41	0.41	0.41	46	72659	73	3	63	7	66
ASE_00332	RNaseP_bact_a links to Rfam database...	0.54	0.51	0.57	71	81686	59	2	51	6	67
ASE_00335	RNaseP_bact_b links to Rfam database...	0.52	0.52	0.52	60	75350	64	13	43	8	56
ASE_00340	RNaseP_bact_a links to Rfam database...	0.71	0.72	0.71	61	45970	34	7	18	9	24
ASE_00353	RNaseP_bact_a links to Rfam database...	0.46	0.47	0.45	50	57860	60	11	49	0	57
ASE_00361	RNaseP_bact_a links to Rfam database...	0.37	0.36	0.38	46	75345	78	9	66	3	81
ASE_00362	RNaseP_bact_a links to Rfam database...	0.62	0.62	0.63	56	48116	36	6	27	3	35
ASE_00363	RNaseP_bact_a links to Rfam database...	0.54	0.55	0.53	52	51262	46	5	41	0	42
ASE_00364	RNaseP_bact_a links to Rfam database...	0.32	0.31	0.33	33	54184	72	7	61	4	72
ASE_00366	RNaseP_bact_a links to Rfam database...	0.52	0.54	0.50	53	58547	55	12	41	2	45
ASE_00367	RNaseP_bact_a links to Rfam database...	0.33	0.35	0.32	30	42976	65	8	57	0	56
ASE_00372	RNaseP_bact_a links to Rfam database...	0.72	0.71	0.72	71	51905	30	5	22	3	29
ASE_00376	RNaseP_bact_a links to Rfam database...	0.52	0.50	0.54	53	56855	48	4	41	3	52
ASE_00382	RNaseP_bact_a links to Rfam database...	0.51	0.51	0.52	43	41822	43	6	34	3	41
ASE_00384	RNaseP_bact_a links to Rfam database...	0.73	0.71	0.75	65	48429	27	4	18	5	27
ASE_00386	RNaseP_bact_a links to Rfam database...	0.53	0.53	0.53	51	50306	51	4	42	5	45
ASE_00387	RNaseP_bact_a links to Rfam database...	0.36	0.37	0.35	38	55837	70	6	64	0	66
ASE_00388	RNaseP_bact_a links to Rfam database...	0.68	0.67	0.69	60	45666	32	1	26	5	29
ASE_00390	RNaseP_bact_a links to Rfam database...	0.50	0.48	0.53	41	42117	44	6	31	7	44
ASE_00393	RNaseP_bact_a links to Rfam database...	0.36	0.34	0.38	32	47810	59	3	50	6	61
ASE_00394	RNaseP_bact_a links to Rfam database...	0.72	0.72	0.73	67	46879	28	3	22	3	26
ASE_00395	RNaseP_bact_a links to Rfam database...	0.51	0.49	0.53	41	41539	45	1	35	9	43
ASE_00396	RNaseP_bact_a links to Rfam database...	0.37	0.36	0.38	30	41536	55	5	45	5	53
ASE_00397	RNaseP_bact_a links to Rfam database...	0.52	0.51	0.52	54	54511	50	7	43	0	51
ASE_00398	RNaseP_bact_a links to Rfam database...	0.64	0.62	0.66	64	55848	36	1	32	3	40
ASE_00400	RNaseP_bact_a links to Rfam database...	0.53	0.52	0.54	55	57868	48	5	42	1	51
ASE_00402	RNaseP_bact_a links to Rfam database...	0.60	0.59	0.61	50	42404	35	4	28	3	35
ASE_00404	RNaseP_bact_a links to Rfam database...	0.56	0.55	0.56	47	42987	42	0	37	5	38
ASE_00406	RNaseP_bact_a links to Rfam database...	0.69	0.66	0.72	62	48742	33	2	22	9	32
ASE_00411	RNaseP_bact_a links to Rfam database...	0.26	0.27	0.26	24	49362	69	12	57	0	65
ASE_00412	RNaseP_bact_a links to Rfam database...	0.38	0.37	0.39	39	58212	60	13	47	0	66
ASE_00416	RNaseP_bact_a links to Rfam database...	0.71	0.68	0.75	86	77306	36	1	28	7	41
ASE_00419	RNaseP_bact_a links to Rfam database...	0.76	0.73	0.80	75	54852	23	4	15	4	28
ASE_00422	RNaseP_bact_a links to Rfam database...	0.48	0.47	0.49	44	46881	51	5	41	5	50
ASE_00423	RNaseP_bact_a links to Rfam database...	0.49	0.49	0.50	53	56847	56	9	44	3	56
ASE_00428	RNaseP_bact_a links to Rfam database...	0.54	0.52	0.57	65	76521	54	5	45	4	60
ASE_00430	RNaseP_bact_a links to Rfam database...	0.63	0.61	0.66	59	46881	36	5	26	5	38
ASE_00437	RNaseP_bact_a links to Rfam database...	0.42	0.41	0.44	55	79275	71	4	67	0	80
ASE_00448	RNaseP_bact_a links to Rfam database...	0.22	0.22	0.23	25	64151	91	6	79	6	87
ASE_00451	RNaseP_bact_a links to Rfam database...	0.50	0.47	0.52	59	70763	57	3	51	3	66
CRW_00177	SSU_rRNA_bacteria links to Rfam database...	0.42	0.41	0.42	196	1178413	284	31	240	13	277
CRW_00250	SSU_rRNA_bacteria links to Rfam database...	0.43	0.43	0.43	205	1198449	287	30	242	15	273
CRW_00278	SSU_rRNA_bacteria links to Rfam database...	0.41	0.40	0.42	180	1129825	270	35	216	19	270
CRW_00280	SSU_rRNA_bacteria links to Rfam database...	0.50	0.50	0.51	226	1117813	234	28	193	13	227
CRW_00789	SSU_rRNA_bacteria links to Rfam database...	0.35	0.35	0.35	156	1137342	304	48	240	16	291
PDB_00571	tRNA links to Rfam database...	0.17	0.16	0.19	4	3300	17	6	11	0	21
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...	0.86	0.75	1.00	18	2260	0	0	0	0	6
PDB_01020	Purine links to Rfam database...	0.23	0.22	0.26	5	2259	14	2	12	0	18
PDB_01073	SAM links to Rfam database...	0.75	0.65	0.88	22	4346	4	0	3	1	12
PDB_01105	SSU_rRNA_bacteria links to Rfam database...	0.51	0.50	0.52	269	1433453	278	27	222	29	271
RFA_00599	Telomerase-vert links to Rfam database...	0.63	0.68	0.60	75	101349	70	18	33	19	36
RFA_00601	Telomerase-vert links to Rfam database...	0.48	0.50	0.46	57	99111	86	21	46	19	57
RFA_00602	Telomerase-vert links to Rfam database...	0.69	0.72	0.67	83	101351	61	10	31	20	33
TMR_00017	tmRNA links to Rfam database...	0.36	0.37	0.36	38	67055	74	15	53	6	64
TMR_00018	tmRNA links to Rfam database...	0.30	0.32	0.30	29	64522	75	10	59	6	63
TMR_00038	tmRNA links to Rfam database...	0.24	0.25	0.24	27	71141	89	12	73	4	83
TMR_00042	tmRNA links to Rfam database...	0.24	0.24	0.24	24	62735	79	9	67	3	74
TMR_00046	tmRNA links to Rfam database...	0.54	0.55	0.54	53	62736	49	11	35	3	43
TMR_00048	tmRNA links to Rfam database...	0.32	0.34	0.30	32	64875	78	9	64	5	63
TMR_00080	tmRNA links to Rfam database...	0.59	0.61	0.56	59	70395	49	16	30	3	37
TMR_00082	tmRNA links to Rfam database...	0.63	0.64	0.63	61	67799	41	12	24	5	35
TMR_00123	tmRNA links to Rfam database...	0.46	0.47	0.46	47	66327	57	11	45	1	54
TMR_00137	tmRNA links to Rfam database...	0.27	0.28	0.26	25	60980	78	14	56	8	64
TMR_00142	tmRNA links to Rfam database...	0.45	0.47	0.44	48	70767	70	15	46	9	54
TMR_00207	tmRNA links to Rfam database...	0.36	0.35	0.36	36	72291	70	4	59	7	67
TMR_00257	tmRNA links to Rfam database...	0.25	0.24	0.26	24	67068	73	8	61	4	74
TMR_00271	tmRNA links to Rfam database...	0.49	0.48	0.49	44	64171	54	8	38	8	47
TMR_00332	tmRNA links to Rfam database...	0.39	0.38	0.40	38	67065	62	9	49	4	61
TMR_00366	tmRNA links to Rfam database...	0.28	0.28	0.29	28	67798	83	12	58	13	72
TMR_00378	tmRNA links to Rfam database...	0.29	0.30	0.28	29	67791	87	7	69	11	68
TMR_00399	tmRNA links to Rfam database...	0.16	0.17	0.15	16	64871	97	27	66	4	78
TMR_00404	tmRNA links to Rfam database...	0.28	0.30	0.26	28	67421	90	22	57	11	64
TMR_00427	tmRNA links to Rfam database...	0.31	0.31	0.31	30	67432	71	11	55	5	67
TMR_00443	tmRNA links to Rfam database...	0.45	0.45	0.46	47	67058	58	14	42	2	57
TMR_00451	tmRNA links to Rfam database...	0.17	0.19	0.16	17	63441	88	16	72	0	72
TMR_00458	tmRNA links to Rfam database...	0.20	0.20	0.20	19	63449	85	19	59	7	74
TMR_00469	tmRNA links to Rfam database...	0.40	0.41	0.38	41	64513	66	11	55	0	59
TMR_00472	tmRNA links to Rfam database...	0.36	0.38	0.35	37	64514	72	24	45	3	60
TMR_00519	tmRNA links to Rfam database...	0.14	0.15	0.13	14	63086	100	16	74	10	81
TMR_00520	tmRNA links to Rfam database...	0.36	0.37	0.35	37	63085	78	13	55	10	62
TMR_00522	tmRNA links to Rfam database...	0.36	0.36	0.36	35	63092	72	11	52	9	62
TMR_00528	tmRNA links to Rfam database...	0.13	0.13	0.12	13	63082	105	12	83	10	84
TMR_00540	tmRNA links to Rfam database...	0.45	0.45	0.46	47	73433	65	4	52	9	57
TMR_00568	tmRNA links to Rfam database...	0.59	0.59	0.60	58	60630	47	3	35	9	41
TMR_00571	tmRNA links to Rfam database...	0.59	0.60	0.58	59	60625	47	7	35	5	40
TMR_00580	tmRNA links to Rfam database...	0.32	0.31	0.32	31	60630	70	13	52	5	69
TMR_00584	tmRNA links to Rfam database...	0.40	0.42	0.38	41	60967	72	8	59	5	56
TMR_00586	tmRNA links to Rfam database...	0.23	0.25	0.22	24	60964	88	18	69	1	73
TMR_00616	tmRNA links to Rfam database...	0.37	0.37	0.36	37	67058	71	18	48	5	62
TMR_00699	tmRNA links to Rfam database...	0.41	0.41	0.41	42	67059	63	10	50	3	60
TMR_00702	tmRNA links to Rfam database...	0.28	0.29	0.28	29	67057	80	18	57	5	71
TMR_00703	tmRNA links to Rfam database...	0.31	0.31	0.31	31	67427	74	16	54	4	68

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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 Murlet(20) - scored higher in this pairwise comparison

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

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

Performance of PknotsRG - scored lower in this pairwise comparison

1. Total counts & total scores for PknotsRG

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