CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	CRWrnafold		Carnac(seed)
MCC	0.599	>	0.415
Average MCC ± 95% Confidence Intervals	0.567 ± 0.057	>	0.323 ± 0.066
Sensitivity	0.584	>	0.196
Positive Predictive Value	0.618	<	0.884
Total TP	1527	>	512
Total TN	436077	<	437968
Total FP	1171	>	145
Total FP CONTRA	159	>	14
Total FP INCONS	784	>	53
Total FP COMP	228	>	78
Total FN	1088	<	2103
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of CRWrnafold 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 CRWrnafold 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 CRWrnafold and Carnac(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for CRWrnafold 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 CRWrnafold and Carnac(seed)).

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Performance of CRWrnafold - scored higher in this pairwise comparison

1. Total counts & total scores for CRWrnafold

Total Base Pair Counts
Total TP	1527
Total TN	436077
Total FP	1171
Total FP CONTRA	159
Total FP INCONS	784
Total FP COMP	228
Total FN	1088

Total Scores
MCC	0.599
Average MCC ± 95% Confidence Intervals	0.567 ± 0.057
Sensitivity	0.584
Positive Predictive Value	0.618
Nr of predictions	123

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_01484	5S_rRNA links to Rfam database...	0.57	0.54	0.62	21	7469	13	0	13	0	18
CRW_01499	5S_rRNA links to Rfam database...	0.58	0.56	0.61	23	7963	16	3	12	1	18
CRW_01603	5S_rRNA links to Rfam database...	0.80	0.76	0.85	28	7107	8	0	5	3	9
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...	0.92	0.85	1.00	35	5015	0	0	0	0	6
PDB_00553	mir-TAR links to Rfam database...	1.00	1.00	1.00	11	454	0	0	0	0	0
PDB_00716	HDV_ribozyme links to Rfam database...	-0.01	0.00	0.00	0	2680	22	0	21	1	23
PDB_00810	s2m links to Rfam database...	0.67	0.59	0.77	10	1068	3	0	3	0	7
PDB_01001	tRNA links to Rfam database...	0.52	0.56	0.50	10	2125	10	3	7	0	8
PDB_01050	UnaL2 links to Rfam database...	0.92	0.85	1.00	11	619	1	0	0	1	2
PDB_01051	Telomerase-cil links to Rfam database...	0.79	0.69	0.90	9	893	5	0	1	4	4
PDB_01092	glmS links to Rfam database...	0.68	0.62	0.76	32	10111	12	1	9	2	20
PDB_01152	HIV_FS2 links to Rfam database...	0.88	0.79	1.00	11	550	0	0	0	0	3
RFA_00389	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00390	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00391	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1418	2	0	0	2	2
RFA_00409	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1418	1	0	0	1	2
RFA_00416	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1470	3	0	0	3	0
RFA_00433	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00434	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00436	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00440	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1470	2	0	0	2	0
RFA_00442	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00446	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1471	2	0	0	2	1
RFA_00449	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1471	2	0	0	2	1
RFA_00587	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	12	0	0	12	0
RFA_00603	Telomerase-cil links to Rfam database...	0.27	0.29	0.26	10	13491	31	8	21	2	25
RFA_00604	Telomerase-cil links to Rfam database...	0.61	0.63	0.59	22	13493	26	2	13	11	13
RFA_00605	Telomerase-cil links to Rfam database...	0.34	0.34	0.34	12	15190	36	4	19	13	23
RFA_00607	Telomerase-cil links to Rfam database...	0.29	0.31	0.28	11	17726	39	5	24	10	25
RFA_00609	Telomerase-cil links to Rfam database...	0.52	0.57	0.48	21	17911	36	8	15	13	16
RFA_00610	Telomerase-cil links to Rfam database...	0.52	0.54	0.50	20	17165	33	4	16	13	17
RFA_00611	Telomerase-cil links to Rfam database...	0.45	0.49	0.43	17	13001	27	8	15	4	18
RFA_00613	Telomerase-cil links to Rfam database...	0.43	0.43	0.44	15	12846	26	8	11	7	20
RFA_00615	Telomerase-cil links to Rfam database...	0.27	0.29	0.26	10	13328	29	7	21	1	25
RFA_00632	HDV_ribozyme links to Rfam database...	0.37	0.36	0.38	10	4069	19	0	16	3	18
RFA_00636	HDV_ribozyme links to Rfam database...	0.51	0.50	0.52	14	3978	13	3	10	0	14
RFA_00642	Vimentin3 links to Rfam database...	0.17	0.17	0.18	3	2909	17	0	14	3	15
RFA_00643	Vimentin3 links to Rfam database...	0.24	0.22	0.27	4	2196	12	2	9	1	14
RFA_00644	Vimentin3 links to Rfam database...	0.21	0.22	0.21	4	2682	15	4	11	0	14
RFA_00645	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2401	14	2	12	0	18
RFA_00649	Vimentin3 links to Rfam database...	0.57	0.56	0.59	10	2128	7	1	6	0	8
RFA_00651	Vimentin3 links to Rfam database...	0.35	0.33	0.38	6	2064	10	1	9	0	12
RFA_00653	Vimentin3 links to Rfam database...	0.35	0.33	0.38	6	2129	10	2	8	0	12
RFA_00654	Vimentin3 links to Rfam database...	0.26	0.28	0.26	5	2396	14	2	12	0	13
RFA_00658	Hammerhead_1 links to Rfam database...	0.59	0.50	0.70	7	1118	4	0	3	1	7
RFA_00659	Hammerhead_1 links to Rfam database...	0.18	0.14	0.25	2	1120	8	0	6	2	12
RFA_00664	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	980	11	0	10	1	14
RFA_00667	Hammerhead_1 links to Rfam database...	0.30	0.29	0.33	4	978	9	1	7	1	10
RFA_00668	Hammerhead_1 links to Rfam database...	0.46	0.43	0.50	6	978	6	0	6	0	8
RFA_00672	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	897	6	0	6	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...	-0.01	0.00	0.00	0	1118	10	0	10	0	14
RFA_00675	Hammerhead_1 links to Rfam database...	0.29	0.29	0.31	4	977	9	1	8	0	10
RFA_00677	Hammerhead_1 links to Rfam database...	0.69	0.64	0.75	9	978	5	0	3	2	5
RFA_00678	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	941	5	0	5	0	14
RFA_00680	Hammerhead_1 links to Rfam database...	0.74	0.71	0.77	10	1115	6	0	3	3	4
RFA_00684	Hammerhead_1 links to Rfam database...	0.72	0.64	0.82	9	979	3	0	2	1	5
RFA_00685	Hammerhead_1 links to Rfam database...	0.42	0.36	0.50	5	980	6	0	5	1	9
RFA_00695	Hammerhead_1 links to Rfam database...	0.67	0.64	0.69	9	7008	28	1	3	24	5
RFA_00703	Hammerhead_1 links to Rfam database...	0.67	0.64	0.69	9	4265	18	1	3	14	5
RFA_00704	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	981	10	0	9	1	14
RFA_00705	Hammerhead_1 links to Rfam database...	0.74	0.71	0.77	10	1022	4	0	3	1	4
RFA_00706	Hammerhead_1 links to Rfam database...	0.33	0.29	0.40	4	1025	6	0	6	0	10
RFA_00707	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1024	11	3	8	0	14
RFA_00708	Hammerhead_1 links to Rfam database...	0.35	0.29	0.44	4	1026	6	0	5	1	10
RFA_00709	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	982	9	0	8	1	14
RFA_00710	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	980	10	0	10	0	14
RFA_00711	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1024	11	0	11	0	14
RFA_00715	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	936	10	0	10	0	14
RFA_00716	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	939	7	0	7	0	14
RFA_00717	Hammerhead_1 links to Rfam database...	0.31	0.29	0.36	4	892	8	0	7	1	10
RFA_00730	s2m links to Rfam database...	0.69	0.67	0.73	8	892	4	1	2	1	4
RFA_00731	s2m links to Rfam database...	0.41	0.42	0.42	5	891	8	3	4	1	7
RFA_00733	s2m links to Rfam database...	0.69	0.67	0.73	8	892	4	1	2	1	4
RFA_00734	s2m links to Rfam database...	0.64	0.67	0.62	8	890	5	1	4	0	4
RFA_00736	s2m links to Rfam database...	0.41	0.42	0.42	5	891	8	3	4	1	7
RFA_00737	s2m links to Rfam database...	0.81	0.67	1.00	8	895	1	0	0	1	4
RFA_00745	s2m links to Rfam database...	0.69	0.67	0.73	8	935	4	1	2	1	4
RFA_00749	s2m links to Rfam database...	0.41	0.42	0.42	5	891	8	3	4	1	7
RFA_00758	s2m links to Rfam database...	0.63	0.58	0.70	7	893	3	1	2	0	5
RFA_00762	s2m links to Rfam database...	0.64	0.67	0.62	8	890	5	1	4	0	4
RFA_00763	s2m links to Rfam database...	0.69	0.67	0.73	8	892	3	1	2	0	4
RFA_00764	s2m links to Rfam database...	0.69	0.67	0.73	8	892	4	1	2	1	4
RFA_00765	s2m links to Rfam database...	0.81	0.67	1.00	8	895	1	0	0	1	4
RFA_00767	Corona_pk3 links to Rfam database...	0.59	0.56	0.63	10	1875	6	3	3	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.47	0.44	0.50	8	1875	8	1	7	0	10
RFA_00769	Corona_pk3 links to Rfam database...	0.54	0.56	0.53	10	1934	9	4	5	0	8
RFA_00770	Corona_pk3 links to Rfam database...	-0.01	0.00	0.00	0	2002	17	1	13	3	18
RFA_00773	Corona_pk3 links to Rfam database...	0.59	0.56	0.63	10	1937	6	1	5	0	8
RFA_00779	Corona_pk3 links to Rfam database...	0.59	0.56	0.63	10	1937	6	3	3	0	8
RFA_00781	Gammaretro_CES links to Rfam database...	0.74	0.75	0.73	24	5017	9	2	7	0	8
RFA_00786	Gammaretro_CES links to Rfam database...	0.17	0.16	0.19	5	5024	21	1	20	0	27
RFA_00791	Gammaretro_CES links to Rfam database...	0.46	0.44	0.48	14	5122	15	0	15	0	18
RFA_00792	Gammaretro_CES links to Rfam database...	0.94	0.94	0.94	30	5018	4	0	2	2	2
RFA_00801	Gammaretro_CES links to Rfam database...	0.38	0.34	0.42	11	5024	16	1	14	1	21
RFA_00808	RydC links to Rfam database...	-0.01	0.00	0.00	0	2000	18	2	14	2	16
RFA_00809	RydC links to Rfam database...	0.40	0.38	0.43	6	2131	8	1	7	0	10
SPR_00020	tRNA links to Rfam database...	0.58	0.60	0.57	12	2680	9	1	8	0	8
SPR_00137	tRNA links to Rfam database...	0.56	0.62	0.52	13	2901	15	4	8	3	8
SPR_00273	tRNA links to Rfam database...	0.31	0.33	0.30	7	2827	17	0	16	1	14
SPR_00394	tRNA links to Rfam database...	0.30	0.33	0.28	7	3630	20	8	10	2	14
SPR_00402	tRNA links to Rfam database...	0.74	0.76	0.73	16	2534	9	0	6	3	5
SPR_00721	tRNA links to Rfam database...	0.98	0.95	1.00	20	2906	2	0	0	2	1
SPR_00816	tRNA links to Rfam database...	0.32	0.35	0.29	7	3462	20	5	12	3	13
SRP_00020	Bacteria_small_SRP links to Rfam database...	0.93	0.94	0.91	31	5531	3	1	2	0	2
SRP_00058	Bacteria_small_SRP links to Rfam database...	0.87	0.88	0.86	30	5743	9	1	4	4	4
SRP_00084	Bacteria_small_SRP links to Rfam database...	0.90	0.91	0.89	31	5425	4	1	3	0	3
SRP_00105	Bacteria_small_SRP links to Rfam database...	0.75	0.76	0.74	26	5530	9	1	8	0	8
SRP_00134	Bacteria_large_SRP links to Rfam database...	0.61	0.66	0.58	19	5962	18	3	11	4	10
SRP_00137	Bacteria_small_SRP links to Rfam database...	0.75	0.84	0.68	21	4155	10	4	6	0	4
SRP_00141	Bacteria_small_SRP links to Rfam database...	0.92	0.93	0.90	38	6286	4	1	3	0	3
SRP_00146	Bacteria_small_SRP links to Rfam database...	0.92	0.92	0.92	33	5217	3	1	2	0	3
SRP_00200	Bacteria_small_SRP links to Rfam database...	0.90	0.92	0.89	33	6866	4	1	3	0	3
SRP_00231	Bacteria_small_SRP links to Rfam database...	0.90	0.91	0.89	31	5425	4	1	3	0	3
SRP_00273	Bacteria_small_SRP links to Rfam database...	0.94	0.95	0.93	38	6745	4	1	2	1	2
SRP_00274	Bacteria_small_SRP links to Rfam database...	0.92	0.92	0.92	35	6865	3	1	2	0	3
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.98	0.97	1.00	29	3712	0	0	0	0	1
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.96	0.94	0.97	34	5425	1	0	1	0	2
SRP_00341	Bacteria_small_SRP links to Rfam database...	0.39	0.39	0.40	12	4723	18	0	18	0	19
SRP_00357	Bacteria_small_SRP links to Rfam database...	0.93	0.94	0.92	34	5319	3	1	2	0	2
SRP_00367	Bacteria_small_SRP links to Rfam database...	0.80	0.83	0.78	29	6749	8	1	7	0	6

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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	512
Total TN	437968
Total FP	145
Total FP CONTRA	14
Total FP INCONS	53
Total FP COMP	78
Total FN	2103

Total Scores
MCC	0.415
Average MCC ± 95% Confidence Intervals	0.323 ± 0.066
Sensitivity	0.196
Positive Predictive Value	0.884
Nr of predictions	123

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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_01484	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7503	0	0	0	0	39
CRW_01499	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	8001	0	0	0	0	41
CRW_01603	5S_rRNA links to Rfam database...	0.00	0.00	0.00	0	7140	0	0	0	0	37
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_01001	tRNA links to Rfam database...	0.00	0.00	0.00	0	2145	0	0	0	0	18
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_00389	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00390	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00391	Hammerhead_3 links to Rfam database...	0.93	0.87	1.00	13	1418	2	0	0	2	2
RFA_00409	Hammerhead_3 links to Rfam database...	0.77	0.60	1.00	9	1422	1	0	0	1	6
RFA_00416	Hammerhead_3 links to Rfam database...	0.93	0.93	0.93	14	1470	4	0	1	3	1
RFA_00433	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00434	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00436	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00440	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1470	2	0	0	2	0
RFA_00442	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
RFA_00446	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1471	2	0	0	2	1
RFA_00449	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1471	2	0	0	2	1
RFA_00587	Y_RNA links to Rfam database...	0.00	0.00	0.00	0	4851	0	0	0	0	15
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_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_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_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_00695	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	7021	0	0	0	0	14
RFA_00703	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	4278	0	0	0	0	14
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_00767	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1881	0	0	0	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1881	0	0	0	0	8
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
SPR_00020	tRNA links to Rfam database...	0.00	0.00	0.00	0	2701	0	0	0	0	20
SPR_00137	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	21
SPR_00273	tRNA links to Rfam database...	0.00	0.00	0.00	0	2850	0	0	0	0	21
SPR_00394	tRNA links to Rfam database...	0.00	0.00	0.00	0	3655	0	0	0	0	21
SPR_00402	tRNA links to Rfam database...	0.00	0.00	0.00	0	2556	0	0	0	0	21
SPR_00721	tRNA links to Rfam database...	0.00	0.00	0.00	0	2926	0	0	0	0	21
SPR_00816	tRNA links to Rfam database...	0.00	0.00	0.00	0	3486	0	0	0	0	20
SRP_00020	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5565	0	0	0	0	33
SRP_00058	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5778	0	0	0	0	34
SRP_00084	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5460	0	0	0	0	34
SRP_00105	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5565	0	0	0	0	34
SRP_00134	Bacteria_large_SRP links to Rfam database...	0.00	0.00	0.00	0	5995	0	0	0	0	29
SRP_00137	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4186	0	0	0	0	25
SRP_00141	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	6328	0	0	0	0	41
SRP_00146	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5253	0	0	0	0	36
SRP_00200	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	6903	0	0	0	0	36
SRP_00231	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5460	0	0	0	0	34
SRP_00273	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	6786	0	0	0	0	40
SRP_00274	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	6903	0	0	0	0	38
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	3741	0	0	0	0	30
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5460	0	0	0	0	36
SRP_00341	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	4753	0	0	0	0	31
SRP_00357	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	5356	0	0	0	0	36
SRP_00367	Bacteria_small_SRP links to Rfam database...	0.00	0.00	0.00	0	6786	0	0	0	0	35

^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 CRWrnafold - scored higher in this pairwise comparison

1. Total counts & total scores for CRWrnafold

2. Individual counts for CRWrnafold [ 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 ]