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(seed)		Carnac(seed)
MCC	0.486	>	0.306
Average MCC ± 95% Confidence Intervals	0.505 ± 0.044	>	0.269 ± 0.057
Sensitivity	0.314	>	0.110
Positive Predictive Value	0.755	<	0.857
Total TP	1849	>	646
Total TN	2787050	<	2788745
Total FP	676	>	194
Total FP CONTRA	38	>	17
Total FP INCONS	562	>	91
Total FP COMP	76	<	86
Total FN	4039	<	5242
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of CMfinder(seed) and Carnac(seed). Positive Predictive Value (PPV) is plotted against sensitivity. Each dot represents a single test of each method. See tables below for raw data (individual counts for CMfinder(seed) and Carnac(seed)).
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(seed) and Carnac(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for CMfinder(seed) and Carnac(seed). The whiskers correspond to 95% confidence intervals (CIs). 'n' denotes the number of MCCs used to calculate average MCCs and CIs. See tables below for raw data (individual counts for CMfinder(seed) and Carnac(seed)).

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

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

Total Base Pair Counts
Total TP	1849
Total TN	2787050
Total FP	676
Total FP CONTRA	38
Total FP INCONS	562
Total FP COMP	76
Total FN	4039

Total Scores
MCC	0.486
Average MCC ± 95% Confidence Intervals	0.505 ± 0.044
Sensitivity	0.314
Positive Predictive Value	0.755
Nr of predictions	127

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_00013	Intron_gpI links to Rfam database...	0.37	0.14	1.00	16	103724	0	0	0	0	99
CRW_00016	Intron_gpI links to Rfam database...	0.36	0.14	0.89	17	77402	2	0	2	0	103
CRW_00610	Intron_gpI links to Rfam database...	0.49	0.31	0.78	25	36283	7	1	6	0	56
CRW_00613	Intron_gpI links to Rfam database...	0.54	0.33	0.87	26	34950	4	0	4	0	52
CRW_00614	Intron_gpI links to Rfam database...	0.46	0.25	0.88	14	121755	9	0	2	7	43
CRW_00618	Intron_gpI links to Rfam database...	0.36	0.13	1.00	8	56272	0	0	0	0	53
CRW_00633	Intron_gpI links to Rfam database...	0.32	0.12	0.81	13	63530	3	1	2	0	93
CRW_00634	Intron_gpI links to Rfam database...	0.40	0.17	0.94	16	64603	1	0	1	0	78
CRW_00670	Intron_gpI links to Rfam database...	0.32	0.18	0.55	22	70085	18	0	18	0	98
CRW_00671	Intron_gpI links to Rfam database...	0.20	0.09	0.41	11	62808	16	0	16	0	106
CRW_00672	Intron_gpI links to Rfam database...	0.38	0.15	0.94	17	72372	1	0	1	0	94
CRW_00674	Intron_gpI links to Rfam database...	0.40	0.17	0.95	21	83414	1	0	1	0	103
CRW_00676	Intron_gpI links to Rfam database...	0.12	0.04	0.33	5	93513	10	1	9	0	110
CRW_00692	Intron_gpI links to Rfam database...	0.41	0.17	1.00	15	68620	0	0	0	0	75
PDB_00005	Tymo_tRNA-like links to Rfam database...	0.47	0.36	0.63	5	938	3	0	3	0	9
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...	0.00	0.00	0.00	0	465	0	0	0	0	11
PDB_00716	HDV_ribozyme links to Rfam database...	-0.01	0.00	0.00	0	2688	13	0	13	0	23
PDB_00810	s2m links to Rfam database...	0.76	0.59	1.00	10	1071	0	0	0	0	7
PDB_00827	Intron_gpI links to Rfam database...	0.25	0.10	0.62	8	27015	5	0	5	0	73
PDB_01050	UnaL2 links to Rfam database...	0.68	0.46	1.00	6	624	1	0	0	1	7
PDB_01051	Telomerase-cil links to Rfam database...	0.83	0.69	1.00	9	894	4	0	0	4	4
PDB_01092	glmS links to Rfam database...	0.38	0.21	0.69	11	10137	6	0	5	1	41
PDB_01152	HIV_FS2 links to Rfam database...	0.92	0.86	1.00	12	549	0	0	0	0	2
RFA_00603	Telomerase-cil links to Rfam database...	0.70	0.60	0.81	21	13504	7	0	5	2	14
RFA_00604	Telomerase-cil links to Rfam database...	0.63	0.51	0.78	18	13507	8	0	5	3	17
RFA_00605	Telomerase-cil links to Rfam database...	0.14	0.06	0.33	2	15219	5	0	4	1	33
RFA_00606	Telomerase-cil links to Rfam database...	0.34	0.21	0.57	8	21307	8	2	4	2	31
RFA_00607	Telomerase-cil links to Rfam database...	0.08	0.06	0.13	2	17750	15	3	11	1	34
RFA_00609	Telomerase-cil links to Rfam database...	0.32	0.22	0.47	8	17938	12	2	7	3	29
RFA_00610	Telomerase-cil links to Rfam database...	0.39	0.30	0.52	11	17184	13	2	8	3	26
RFA_00611	Telomerase-cil links to Rfam database...	0.65	0.51	0.82	18	13019	5	0	4	1	17
RFA_00613	Telomerase-cil links to Rfam database...	0.70	0.57	0.87	20	12857	4	0	3	1	15
RFA_00615	Telomerase-cil links to Rfam database...	0.57	0.49	0.68	17	13341	10	0	8	2	18
RFA_00620	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	21939	6	0	6	0	39
RFA_00626	rne5 links to Rfam database...	0.44	0.32	0.60	28	56569	22	2	17	3	59
RFA_00627	rne5 links to Rfam database...	0.53	0.39	0.72	34	56906	15	3	10	2	53
RFA_00628	rne5 links to Rfam database...	0.58	0.43	0.77	37	57243	14	3	8	3	49
RFA_00630	rne5 links to Rfam database...	0.45	0.32	0.64	28	56909	17	3	13	1	59
RFA_00632	HDV_ribozyme links to Rfam database...	0.27	0.25	0.29	7	4071	17	0	17	0	21
RFA_00636	HDV_ribozyme links to Rfam database...	0.71	0.64	0.78	18	3982	5	2	3	0	10
RFA_00639	7SK links to Rfam database...	0.00	0.00	0.00	0	54575	44	6	34	4	87
RFA_00642	Vimentin3 links to Rfam database...	0.44	0.28	0.71	5	2919	2	0	2	0	13
RFA_00643	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2203	8	0	8	0	18
RFA_00644	Vimentin3 links to Rfam database...	0.00	0.00	0.00	0	2693	8	0	8	0	18
RFA_00645	Vimentin3 links to Rfam database...	0.29	0.17	0.50	3	2409	3	0	3	0	15
RFA_00649	Vimentin3 links to Rfam database...	0.35	0.22	0.57	4	2138	3	0	3	0	14
RFA_00651	Vimentin3 links to Rfam database...	0.35	0.22	0.57	4	2073	3	0	3	0	14
RFA_00653	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2137	8	0	8	0	18
RFA_00654	Vimentin3 links to Rfam database...	0.38	0.22	0.67	4	2409	2	0	2	0	14
RFA_00658	Hammerhead_1 links to Rfam database...	0.40	0.29	0.57	4	1121	4	0	3	1	10
RFA_00659	Hammerhead_1 links to Rfam database...	0.23	0.14	0.40	2	1123	4	0	3	1	12
RFA_00664	Hammerhead_1 links to Rfam database...	0.40	0.29	0.57	4	983	4	0	3	1	10
RFA_00667	Hammerhead_1 links to Rfam database...	0.40	0.29	0.57	4	983	4	0	3	1	10
RFA_00668	Hammerhead_1 links to Rfam database...	0.35	0.21	0.60	3	985	3	0	2	1	11
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...	0.23	0.14	0.40	2	1123	4	0	3	1	12
RFA_00674	Hammerhead_1 links to Rfam database...	0.40	0.29	0.57	4	1121	4	0	3	1	10
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...	0.40	0.29	0.57	4	983	4	0	3	1	10
RFA_00678	Hammerhead_1 links to Rfam database...	0.43	0.29	0.67	4	940	3	0	2	1	10
RFA_00680	Hammerhead_1 links to Rfam database...	0.40	0.29	0.57	4	1121	4	0	3	1	10
RFA_00684	Hammerhead_1 links to Rfam database...	0.43	0.29	0.67	4	984	3	0	2	1	10
RFA_00685	Hammerhead_1 links to Rfam database...	0.32	0.21	0.50	3	984	4	0	3	1	11
RFA_00704	Hammerhead_1 links to Rfam database...	0.32	0.21	0.50	3	984	4	0	3	1	11
RFA_00705	Hammerhead_1 links to Rfam database...	0.40	0.29	0.57	4	1028	4	0	3	1	10
RFA_00706	Hammerhead_1 links to Rfam database...	0.43	0.29	0.67	4	1029	3	0	2	1	10
RFA_00707	Hammerhead_1 links to Rfam database...	0.43	0.29	0.67	4	1029	3	0	2	1	10
RFA_00708	Hammerhead_1 links to Rfam database...	0.40	0.29	0.57	4	1028	4	0	3	1	10
RFA_00709	Hammerhead_1 links to Rfam database...	0.32	0.21	0.50	3	984	4	0	3	1	11
RFA_00710	Hammerhead_1 links to Rfam database...	0.32	0.21	0.50	3	984	3	0	3	0	11
RFA_00711	Hammerhead_1 links to Rfam database...	0.43	0.29	0.67	4	1029	3	0	2	1	10
RFA_00715	Hammerhead_1 links to Rfam database...	0.30	0.14	0.67	2	943	2	0	1	1	12
RFA_00716	Hammerhead_1 links to Rfam database...	0.43	0.29	0.67	4	940	3	0	2	1	10
RFA_00717	Hammerhead_1 links to Rfam database...	0.30	0.21	0.43	3	896	4	0	4	0	11
RFA_00730	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00731	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00733	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00734	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00736	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00737	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00745	s2m links to Rfam database...	0.91	0.83	1.00	10	936	0	0	0	0	2
RFA_00749	s2m links to Rfam database...	0.91	0.83	1.00	10	893	0	0	0	0	2
RFA_00758	s2m links to Rfam database...	0.86	0.75	1.00	9	894	0	0	0	0	3
RFA_00762	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_00764	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
RFA_00769	Corona_pk3 links to Rfam database...	0.71	0.50	1.00	9	1944	0	0	0	0	9
RFA_00770	Corona_pk3 links to Rfam database...	0.71	0.50	1.00	9	2007	0	0	0	0	9
RFA_00773	Corona_pk3 links to Rfam database...	0.00	0.00	0.00	0	1949	4	0	4	0	18
RFA_00779	Corona_pk3 links to Rfam database...	0.71	0.50	1.00	9	1944	0	0	0	0	9
RFA_00781	Gammaretro_CES links to Rfam database...	0.97	0.94	1.00	30	5020	0	0	0	0	2
RFA_00786	Gammaretro_CES links to Rfam database...	0.95	0.91	1.00	29	5021	0	0	0	0	3
RFA_00791	Gammaretro_CES links to Rfam database...	0.92	0.88	0.97	28	5122	1	0	1	0	4
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...	0.95	0.91	1.00	29	5021	0	0	0	0	3
RFA_00808	RydC links to Rfam database...	0.68	0.56	0.82	9	2005	2	0	2	0	7
RFA_00809	RydC links to Rfam database...	0.41	0.38	0.46	6	2132	7	1	6	0	10
RFA_00814	R2_retro_el links to Rfam database...	0.68	0.51	0.91	21	25177	2	0	2	0	20
RFA_00815	R2_retro_el links to Rfam database...	0.68	0.51	0.91	21	24508	2	0	2	0	20
RFA_00816	R2_retro_el links to Rfam database...	0.68	0.51	0.91	21	23197	2	0	2	0	20
RFA_00817	R2_retro_el links to Rfam database...	0.68	0.56	0.82	23	21917	5	0	5	0	18
RFA_00818	R2_retro_el links to Rfam database...	0.60	0.49	0.74	20	20274	8	1	6	1	21
RFA_00819	R2_retro_el links to Rfam database...	0.62	0.51	0.75	21	27938	7	0	7	0	20
SRP_00016	Archaea_SRP links to Rfam database...	0.54	0.35	0.83	38	47849	8	0	8	0	71
SRP_00130	Archaea_SRP links to Rfam database...	0.50	0.32	0.78	31	49730	10	1	8	1	66
SRP_00142	Archaea_SRP links to Rfam database...	0.46	0.37	0.58	34	45997	26	1	24	1	59
SRP_00143	Archaea_SRP links to Rfam database...	0.50	0.30	0.86	30	49735	5	0	5	0	71
SRP_00144	Archaea_SRP links to Rfam database...	0.54	0.37	0.80	35	46621	11	0	9	2	59
SRP_00197	Archaea_SRP links to Rfam database...	0.46	0.26	0.84	26	49424	5	0	5	0	75
SRP_00198	Archaea_SRP links to Rfam database...	0.56	0.37	0.84	38	50995	7	0	7	0	65
SRP_00199	Archaea_SRP links to Rfam database...	0.54	0.35	0.82	37	50995	8	0	8	0	68
SRP_00201	Archaea_SRP links to Rfam database...	0.54	0.35	0.83	39	47848	8	0	8	0	72
SRP_00202	Archaea_SRP links to Rfam database...	0.43	0.21	0.86	25	54256	4	0	4	0	92
SRP_00203	Archaea_SRP links to Rfam database...	0.51	0.34	0.77	36	48781	12	0	11	1	69
SRP_00204	Archaea_SRP links to Rfam database...	0.52	0.34	0.80	35	49097	9	1	8	0	67
SRP_00206	Archaea_SRP links to Rfam database...	0.55	0.36	0.83	39	47848	8	0	8	0	69
SRP_00255	Archaea_SRP links to Rfam database...	0.49	0.27	0.89	25	47558	3	0	3	0	69
SRP_00276	Archaea_SRP links to Rfam database...	0.51	0.33	0.80	36	50676	9	0	9	0	74
SRP_00278	Archaea_SRP links to Rfam database...	0.52	0.33	0.81	35	46013	8	0	8	0	70
SRP_00322	Archaea_SRP links to Rfam database...	0.52	0.33	0.82	36	48472	8	0	8	0	73
SRP_00323	Archaea_SRP links to Rfam database...	0.54	0.34	0.88	36	47237	5	0	5	0	71
SRP_00330	Archaea_SRP links to Rfam database...	0.44	0.23	0.85	22	50060	5	0	4	1	73
SRP_00332	Archaea_SRP links to Rfam database...	0.44	0.25	0.75	27	50367	9	0	9	0	79
SRP_00339	Archaea_SRP links to Rfam database...	0.56	0.39	0.79	37	44504	10	2	8	0	57

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Performance of Carnac(seed) - scored lower in this pairwise comparison

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

Total Base Pair Counts
Total TP	646
Total TN	2788745
Total FP	194
Total FP CONTRA	17
Total FP INCONS	91
Total FP COMP	86
Total FN	5242

Total Scores
MCC	0.306
Average MCC ± 95% Confidence Intervals	0.269 ± 0.057
Sensitivity	0.110
Positive Predictive Value	0.857
Nr of predictions	127

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_00013	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	103740	0	0	0	0	115
CRW_00016	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	77421	0	0	0	0	120
CRW_00610	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	36315	0	0	0	0	81
CRW_00613	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	34980	0	0	0	0	78
CRW_00614	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	121771	0	0	0	0	57
CRW_00618	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	56280	0	0	0	0	61
CRW_00633	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	63546	0	0	0	0	106
CRW_00634	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	64620	0	0	0	0	94
CRW_00670	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	70125	0	0	0	0	120
CRW_00671	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	62835	0	0	0	0	117
CRW_00672	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	72390	0	0	0	0	111
CRW_00674	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	83436	0	0	0	0	124
CRW_00676	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	93528	0	0	0	0	115
CRW_00692	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	68635	0	0	0	0	90
PDB_00005	Tymo_tRNA-like links to Rfam database...	0.88	0.79	1.00	11	935	0	0	0	0	3
PDB_00012	mir-TAR links to Rfam database...	1.00	1.00	1.00	7	399	3	0	0	3	0
PDB_00213	Gammaretro_CES links to Rfam database...	0.58	0.34	1.00	14	5036	0	0	0	0	27
PDB_00553	mir-TAR links to Rfam database...	0.79	0.64	1.00	7	458	0	0	0	0	4
PDB_00716	HDV_ribozyme links to Rfam database...	0.00	0.00	0.00	0	2701	0	0	0	0	23
PDB_00810	s2m links to Rfam database...	0.64	0.41	1.00	7	1074	0	0	0	0	10
PDB_00827	Intron_gpI links to Rfam database...	0.00	0.00	0.00	0	27028	0	0	0	0	81
PDB_01050	UnaL2 links to Rfam database...	0.62	0.38	1.00	5	625	1	0	0	1	8
PDB_01051	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	903	0	0	0	0	13
PDB_01092	glmS links to Rfam database...	0.77	0.63	0.94	33	10118	3	1	1	1	19
PDB_01152	HIV_FS2 links to Rfam database...	0.88	0.79	1.00	11	550	0	0	0	0	3
RFA_00603	Telomerase-cil links to Rfam database...	0.56	0.31	1.00	11	13519	2	0	0	2	24
RFA_00604	Telomerase-cil links to Rfam database...	0.56	0.31	1.00	11	13519	6	0	0	6	24
RFA_00605	Telomerase-cil links to Rfam database...	0.41	0.17	1.00	6	15219	2	0	0	2	29
RFA_00606	Telomerase-cil links to Rfam database...	0.17	0.08	0.38	3	21313	6	1	4	1	36
RFA_00607	Telomerase-cil links to Rfam database...	0.25	0.08	0.75	3	17762	10	0	1	9	33
RFA_00609	Telomerase-cil links to Rfam database...	0.27	0.14	0.56	5	17946	10	2	2	6	32
RFA_00610	Telomerase-cil links to Rfam database...	0.37	0.14	1.00	5	17200	5	0	0	5	32
RFA_00611	Telomerase-cil links to Rfam database...	0.38	0.14	1.00	5	13036	0	0	0	0	30
RFA_00613	Telomerase-cil links to Rfam database...	0.24	0.14	0.42	5	12868	7	4	3	0	30
RFA_00615	Telomerase-cil links to Rfam database...	0.48	0.23	1.00	8	13358	1	0	0	1	27
RFA_00620	Telomerase-cil links to Rfam database...	0.13	0.08	0.23	3	21932	11	2	8	1	36
RFA_00626	rne5 links to Rfam database...	0.67	0.52	0.87	45	56564	11	0	7	4	42
RFA_00627	rne5 links to Rfam database...	0.69	0.55	0.86	48	56897	10	0	8	2	39
RFA_00628	rne5 links to Rfam database...	0.66	0.43	1.00	37	57254	6	0	0	6	49
RFA_00630	rne5 links to Rfam database...	0.79	0.67	0.94	58	56891	12	0	4	8	29
RFA_00632	HDV_ribozyme links to Rfam database...	0.00	0.00	0.00	0	4095	0	0	0	0	28
RFA_00636	HDV_ribozyme links to Rfam database...	0.00	0.00	0.00	0	4005	0	0	0	0	28
RFA_00639	7SK links to Rfam database...	0.00	0.00	0.00	0	54608	7	0	7	0	87
RFA_00642	Vimentin3 links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	18
RFA_00643	Vimentin3 links to Rfam database...	0.00	0.00	0.00	0	2211	0	0	0	0	18
RFA_00644	Vimentin3 links to Rfam database...	0.00	0.00	0.00	0	2701	0	0	0	0	18
RFA_00645	Vimentin3 links to Rfam database...	0.00	0.00	0.00	0	2415	0	0	0	0	18
RFA_00649	Vimentin3 links to Rfam database...	0.00	0.00	0.00	0	2145	0	0	0	0	18
RFA_00651	Vimentin3 links to Rfam database...	0.00	0.00	0.00	0	2080	0	0	0	0	18
RFA_00653	Vimentin3 links to Rfam database...	0.00	0.00	0.00	0	2145	0	0	0	0	18
RFA_00654	Vimentin3 links to Rfam database...	0.00	0.00	0.00	0	2415	0	0	0	0	18
RFA_00658	Hammerhead_1 links to Rfam database...	0.40	0.29	0.57	4	1121	5	0	3	2	10
RFA_00659	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1124	4	0	4	0	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	985	5	1	4	0	14
RFA_00668	Hammerhead_1 links to Rfam database...	0.50	0.43	0.60	6	980	4	0	4	0	8
RFA_00672	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	903	0	0	0	0	13
RFA_00673	Hammerhead_1 links to Rfam database...	0.47	0.36	0.63	5	1120	4	0	3	1	9
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...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00677	Hammerhead_1 links to Rfam database...	0.53	0.43	0.67	6	981	4	0	3	1	8
RFA_00678	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	946	0	0	0	0	14
RFA_00680	Hammerhead_1 links to Rfam database...	0.84	0.71	1.00	10	1118	2	0	0	2	4
RFA_00684	Hammerhead_1 links to Rfam database...	0.84	0.71	1.00	10	980	1	0	0	1	4
RFA_00685	Hammerhead_1 links to Rfam database...	0.59	0.36	1.00	5	985	0	0	0	0	9
RFA_00704	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00705	Hammerhead_1 links to Rfam database...	0.84	0.71	1.00	10	1025	0	0	0	0	4
RFA_00706	Hammerhead_1 links to Rfam database...	0.53	0.29	1.00	4	1031	0	0	0	0	10
RFA_00707	Hammerhead_1 links to Rfam database...	0.53	0.29	1.00	4	1031	0	0	0	0	10
RFA_00708	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1035	0	0	0	0	14
RFA_00709	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	984	7	0	6	1	14
RFA_00710	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	987	3	0	3	0	14
RFA_00711	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1031	4	0	4	0	14
RFA_00715	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	943	3	1	2	0	14
RFA_00716	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...	0.64	0.42	1.00	5	898	1	0	0	1	7
RFA_00731	s2m links to Rfam database...	0.64	0.42	1.00	5	898	1	0	0	1	7
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...	0.64	0.42	1.00	5	898	1	0	0	1	7
RFA_00737	s2m links to Rfam database...	0.64	0.42	1.00	5	898	1	0	0	1	7
RFA_00745	s2m links to Rfam database...	0.64	0.42	1.00	5	941	1	0	0	1	7
RFA_00749	s2m links to Rfam database...	0.64	0.42	1.00	5	898	1	0	0	1	7
RFA_00758	s2m links to Rfam database...	0.00	0.00	0.00	0	903	0	0	0	0	12
RFA_00762	s2m links to Rfam database...	0.64	0.42	1.00	5	898	0	0	0	0	7
RFA_00763	s2m links to Rfam database...	0.64	0.42	1.00	5	898	1	0	0	1	7
RFA_00764	s2m links to Rfam database...	0.64	0.42	1.00	5	898	1	0	0	1	7
RFA_00765	s2m links to Rfam database...	0.64	0.42	1.00	5	898	1	0	0	1	7
RFA_00769	Corona_pk3 links to Rfam database...	0.71	0.56	0.91	10	1942	1	1	0	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.62	0.39	1.00	7	2009	0	0	0	0	11
RFA_00773	Corona_pk3 links to Rfam database...	0.71	0.56	0.91	10	1942	1	1	0	0	8
RFA_00779	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1943	0	0	0	0	8
RFA_00781	Gammaretro_CES links to Rfam database...	0.25	0.13	0.50	4	5042	4	1	3	0	28
RFA_00786	Gammaretro_CES links to Rfam database...	0.25	0.13	0.50	4	5042	4	1	3	0	28
RFA_00791	Gammaretro_CES links to Rfam database...	0.00	0.00	0.00	0	5151	0	0	0	0	32
RFA_00792	Gammaretro_CES links to Rfam database...	0.00	0.00	0.00	0	5046	4	1	3	0	32
RFA_00801	Gammaretro_CES links to Rfam database...	0.00	0.00	0.00	0	5050	0	0	0	0	32
RFA_00808	RydC links to Rfam database...	0.00	0.00	0.00	0	2016	0	0	0	0	16
RFA_00809	RydC links to Rfam database...	0.00	0.00	0.00	0	2145	0	0	0	0	16
RFA_00814	R2_retro_el links to Rfam database...	0.66	0.44	1.00	18	25182	2	0	0	2	23
RFA_00815	R2_retro_el links to Rfam database...	0.75	0.56	1.00	23	24508	1	0	0	1	18
RFA_00816	R2_retro_el links to Rfam database...	0.66	0.44	1.00	18	23202	2	0	0	2	23
RFA_00817	R2_retro_el links to Rfam database...	0.80	0.66	0.96	27	21917	1	0	1	0	14
RFA_00818	R2_retro_el links to Rfam database...	0.70	0.49	1.00	20	20281	3	0	0	3	21
RFA_00819	R2_retro_el links to Rfam database...	0.75	0.56	1.00	23	27943	2	0	0	2	18
SRP_00016	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	47895	0	0	0	0	109
SRP_00130	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	49770	0	0	0	0	97
SRP_00142	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	46056	0	0	0	0	93
SRP_00143	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	49770	0	0	0	0	101
SRP_00144	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	46665	0	0	0	0	94
SRP_00197	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	49455	0	0	0	0	101
SRP_00198	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	51040	0	0	0	0	103
SRP_00199	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	51040	0	0	0	0	105
SRP_00201	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	47895	0	0	0	0	111
SRP_00202	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	54285	0	0	0	0	117
SRP_00203	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	48828	0	0	0	0	105
SRP_00204	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	49141	0	0	0	0	102
SRP_00206	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	47895	0	0	0	0	108
SRP_00255	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	47586	0	0	0	0	94
SRP_00276	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	50721	0	0	0	0	110
SRP_00278	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	46056	0	0	0	0	105
SRP_00322	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	48516	0	0	0	0	109
SRP_00323	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	47278	0	0	0	0	107
SRP_00330	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	50086	0	0	0	0	95
SRP_00332	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	50403	0	0	0	0	106
SRP_00339	Archaea_SRP links to Rfam database...	0.00	0.00	0.00	0	44551	0	0	0	0	94

^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(seed) - scored higher in this pairwise comparison

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

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

Performance of Carnac(seed) - scored lower in this pairwise comparison

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

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