CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	ContextFold		Murlet(seed)
MCC	0.761	>	0.540
Average MCC ± 95% Confidence Intervals	0.712 ± 0.051	>	0.396 ± 0.065
Sensitivity	0.727	>	0.360
Positive Predictive Value	0.798	<	0.811
Total TP	3510	>	1738
Total TN	2787240	<	2789495
Total FP	1164	>	489
Total FP CONTRA	177	>	21
Total FP INCONS	712	>	385
Total FP COMP	275	>	83
Total FN	1318	<	3090
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of ContextFold and Murlet(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 ContextFold and Murlet(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 ContextFold and Murlet(seed)).
Comparison of average Matthews Correlation Coefficients (MCCs) for ContextFold and Murlet(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 ContextFold and Murlet(seed)).

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Performance of ContextFold - scored higher in this pairwise comparison

1. Total counts & total scores for ContextFold

Total Base Pair Counts
Total TP	3510
Total TN	2787240
Total FP	1164
Total FP CONTRA	177
Total FP INCONS	712
Total FP COMP	275
Total FN	1318

Total Scores
MCC	0.761
Average MCC ± 95% Confidence Intervals	0.712 ± 0.051
Sensitivity	0.727
Positive Predictive Value	0.798
Nr of predictions	123

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_01343	SSU_rRNA_archaea links to Rfam database...	0.82	0.76	0.89	328	977531	59	6	36	17	106
PDB_00005	Tymo_tRNA-like links to Rfam database...	0.42	0.36	0.50	5	936	5	0	5	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...	0.90	0.85	0.95	35	5013	2	0	2	0	6
PDB_00553	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	455	0	0	0	0	1
PDB_00716	HDV_ribozyme links to Rfam database...	-0.01	0.00	0.00	0	2687	14	0	14	0	23
PDB_00810	s2m links to Rfam database...	0.91	0.82	1.00	14	1067	0	0	0	0	3
PDB_01050	UnaL2 links to Rfam database...	0.96	0.92	1.00	12	618	1	0	0	1	1
PDB_01051	Telomerase-cil links to Rfam database...	0.96	0.92	1.00	12	891	4	0	0	4	1
PDB_01092	glmS links to Rfam database...	0.70	0.63	0.77	33	10110	12	1	9	2	19
PDB_01152	HIV_FS2 links to Rfam database...	0.88	0.79	1.00	11	550	0	0	0	0	3
RFA_00390	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	0	0	0	0	0
RFA_00416	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1470	1	0	0	1	0
RFA_00433	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	0	0	0	0	0
RFA_00587	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	11	0	0	11	0
RFA_00603	Telomerase-cil links to Rfam database...	0.63	0.60	0.66	21	13498	12	5	6	1	14
RFA_00604	Telomerase-cil links to Rfam database...	0.73	0.69	0.77	24	13499	17	2	5	10	11
RFA_00605	Telomerase-cil links to Rfam database...	0.20	0.17	0.24	6	15200	26	5	14	7	29
RFA_00606	Telomerase-cil links to Rfam database...	0.45	0.44	0.47	17	21285	23	10	9	4	22
RFA_00607	Telomerase-cil links to Rfam database...	0.85	0.75	0.96	27	17738	10	0	1	9	9
RFA_00609	Telomerase-cil links to Rfam database...	0.68	0.65	0.71	24	17921	17	2	8	7	13
RFA_00610	Telomerase-cil links to Rfam database...	0.90	0.86	0.94	32	17171	7	0	2	5	5
RFA_00611	Telomerase-cil links to Rfam database...	0.93	0.86	1.00	30	13011	0	0	0	0	5
RFA_00613	Telomerase-cil links to Rfam database...	0.68	0.66	0.70	23	12847	11	4	6	1	12
RFA_00615	Telomerase-cil links to Rfam database...	0.67	0.60	0.75	21	13338	7	6	1	0	14
RFA_00620	Telomerase-cil links to Rfam database...	0.58	0.54	0.62	21	21911	27	3	10	14	18
RFA_00626	rne5 links to Rfam database...	0.80	0.75	0.87	65	56541	19	1	9	9	22
RFA_00627	rne5 links to Rfam database...	0.76	0.71	0.81	62	56876	16	3	12	1	25
RFA_00628	rne5 links to Rfam database...	0.60	0.56	0.65	48	57217	28	3	23	2	38
RFA_00630	rne5 links to Rfam database...	0.62	0.60	0.65	52	56873	35	3	25	7	35
RFA_00632	HDV_ribozyme links to Rfam database...	0.25	0.25	0.26	7	4068	20	1	19	0	21
RFA_00636	HDV_ribozyme links to Rfam database...	0.52	0.43	0.63	12	3986	7	0	7	0	16
RFA_00639	7SK links to Rfam database...	0.64	0.63	0.65	55	54531	39	7	22	10	32
RFA_00642	Vimentin3 links to Rfam database...	0.44	0.39	0.50	7	2912	7	2	5	0	11
RFA_00643	Vimentin3 links to Rfam database...	0.47	0.39	0.58	7	2199	5	0	5	0	11
RFA_00644	Vimentin3 links to Rfam database...	0.77	0.83	0.71	15	2680	6	3	3	0	3
RFA_00645	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2402	13	2	11	0	18
RFA_00649	Vimentin3 links to Rfam database...	0.88	0.83	0.94	15	2129	1	0	1	0	3
RFA_00651	Vimentin3 links to Rfam database...	0.59	0.50	0.69	9	2067	4	0	4	0	9
RFA_00653	Vimentin3 links to Rfam database...	0.25	0.22	0.29	4	2131	10	2	8	0	14
RFA_00654	Vimentin3 links to Rfam database...	0.71	0.67	0.75	12	2399	5	1	3	1	6
RFA_00658	Hammerhead_1 links to Rfam database...	0.89	0.79	1.00	11	1117	0	0	0	0	3
RFA_00659	Hammerhead_1 links to Rfam database...	0.53	0.43	0.67	6	1119	3	0	3	0	8
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...	0.33	0.29	0.40	4	980	7	0	6	1	10
RFA_00668	Hammerhead_1 links to Rfam database...	0.67	0.57	0.80	8	980	2	0	2	0	6
RFA_00672	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	895	8	0	8	0	13
RFA_00673	Hammerhead_1 links to Rfam database...	0.80	0.64	1.00	9	1119	0	0	0	0	5
RFA_00674	Hammerhead_1 links to Rfam database...	0.92	0.86	1.00	12	1116	1	0	0	1	2
RFA_00675	Hammerhead_1 links to Rfam database...	0.80	0.64	1.00	9	981	0	0	0	0	5
RFA_00677	Hammerhead_1 links to Rfam database...	0.67	0.57	0.80	8	980	2	0	2	0	6
RFA_00678	Hammerhead_1 links to Rfam database...	0.84	0.71	1.00	10	936	0	0	0	0	4
RFA_00680	Hammerhead_1 links to Rfam database...	0.92	0.86	1.00	12	1116	1	0	0	1	2
RFA_00684	Hammerhead_1 links to Rfam database...	0.77	0.71	0.83	10	978	2	0	2	0	4
RFA_00685	Hammerhead_1 links to Rfam database...	0.71	0.57	0.89	8	981	1	0	1	0	6
RFA_00695	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	7006	23	2	13	8	14
RFA_00703	Hammerhead_1 links to Rfam database...	0.46	0.43	0.50	6	4266	14	0	6	8	8
RFA_00704	Hammerhead_1 links to Rfam database...	0.50	0.43	0.60	6	980	5	0	4	1	8
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...	0.84	0.71	1.00	10	1025	0	0	0	0	4
RFA_00707	Hammerhead_1 links to Rfam database...	0.89	0.79	1.00	11	1024	0	0	0	0	3
RFA_00708	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1029	6	0	6	0	14
RFA_00709	Hammerhead_1 links to Rfam database...	0.16	0.14	0.20	2	980	9	0	8	1	12
RFA_00710	Hammerhead_1 links to Rfam database...	0.40	0.36	0.45	5	979	6	0	6	0	9
RFA_00711	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1024	12	0	11	1	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	938	8	0	8	0	14
RFA_00717	Hammerhead_1 links to Rfam database...	0.88	0.79	1.00	11	892	0	0	0	0	3
RFA_00730	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00731	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00733	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00734	s2m links to Rfam database...	0.78	0.75	0.82	9	892	3	0	2	1	3
RFA_00736	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00737	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00745	s2m links to Rfam database...	1.00	1.00	1.00	12	934	1	0	0	1	0
RFA_00749	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00758	s2m links to Rfam database...	0.96	0.92	1.00	11	892	0	0	0	0	1
RFA_00762	s2m links to Rfam database...	0.96	0.92	1.00	11	892	0	0	0	0	1
RFA_00763	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00764	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00765	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
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...	0.61	0.56	0.67	10	1876	5	2	3	0	8
RFA_00769	Corona_pk3 links to Rfam database...	0.55	0.56	0.56	10	1935	8	4	4	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.61	0.56	0.67	10	2001	5	2	3	0	8
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...	0.61	0.56	0.67	10	1938	5	2	3	0	8
RFA_00781	Gammaretro_CES links to Rfam database...	1.00	1.00	1.00	32	5018	0	0	0	0	0
RFA_00786	Gammaretro_CES links to Rfam database...	0.97	0.94	1.00	30	5020	0	0	0	0	2
RFA_00791	Gammaretro_CES links to Rfam database...	0.94	0.88	1.00	28	5123	1	0	0	1	4
RFA_00792	Gammaretro_CES links to Rfam database...	0.76	0.75	0.77	24	5019	7	2	5	0	8
RFA_00801	Gammaretro_CES links to Rfam database...	0.97	0.94	1.00	30	5020	1	0	0	1	2
RFA_00808	RydC links to Rfam database...	0.58	0.44	0.78	7	2007	2	0	2	0	9
RFA_00809	RydC links to Rfam database...	0.39	0.31	0.50	5	2135	6	0	5	1	11
RFA_00814	R2_retro_el links to Rfam database...	0.94	0.93	0.95	38	25160	18	0	2	16	3
RFA_00815	R2_retro_el links to Rfam database...	0.74	0.83	0.65	34	24479	21	13	5	3	7
RFA_00816	R2_retro_el links to Rfam database...	0.67	0.71	0.63	29	23174	22	13	4	5	12
RFA_00817	R2_retro_el links to Rfam database...	0.58	0.59	0.59	24	21904	17	5	12	0	17
RFA_00818	R2_retro_el links to Rfam database...	0.61	0.66	0.56	27	20253	29	10	11	8	14
RFA_00819	R2_retro_el links to Rfam database...	0.96	0.95	0.98	39	27926	15	0	1	14	2
RFA_00820	bicoid_3 links to Rfam database...	0.94	0.92	0.97	147	151373	9	1	4	4	13
RFA_00830	bicoid_3 links to Rfam database...	0.54	0.47	0.62	73	152510	80	5	40	35	81
SRP_00079	Plant_SRP links to Rfam database...	0.87	0.85	0.89	75	41821	17	0	9	8	13
SRP_00124	Metazoa_SRP links to Rfam database...	0.90	0.87	0.94	74	37049	9	0	5	4	11
SRP_00137	Bacteria_small_SRP links to Rfam database...	0.77	0.80	0.74	20	4159	7	3	4	0	5
SRP_00141	Bacteria_small_SRP links to Rfam database...	0.99	0.98	1.00	40	6288	0	0	0	0	1
SRP_00146	Bacteria_small_SRP links to Rfam database...	1.00	1.00	1.00	36	5217	0	0	0	0	0
SRP_00182	Plant_SRP links to Rfam database...	0.86	0.83	0.88	84	45961	11	2	9	0	17
SRP_00197	Archaea_SRP links to Rfam database...	0.91	0.88	0.95	89	49361	5	0	5	0	12
SRP_00198	Archaea_SRP links to Rfam database...	0.91	0.88	0.95	91	50944	5	0	5	0	12
SRP_00199	Archaea_SRP links to Rfam database...	0.86	0.84	0.89	88	50941	12	0	11	1	17
SRP_00202	Archaea_SRP links to Rfam database...	0.97	0.97	0.98	113	54170	3	0	2	1	4
SRP_00241	Plant_SRP links to Rfam database...	0.55	0.59	0.53	48	45965	44	14	29	1	34
SRP_00255	Archaea_SRP links to Rfam database...	0.85	0.86	0.84	81	47489	19	0	16	3	13
SRP_00260	Metazoa_SRP links to Rfam database...	0.68	0.68	0.68	68	47795	34	5	27	2	32
SRP_00278	Archaea_SRP links to Rfam database...	0.83	0.82	0.85	86	45955	15	0	15	0	19
SRP_00285	Bacteria_small_SRP links to Rfam database...	1.00	1.00	1.00	30	3711	0	0	0	0	0
SRP_00322	Archaea_SRP links to Rfam database...	0.94	0.94	0.94	102	48408	6	0	6	0	7
SRP_00328	Metazoa_SRP links to Rfam database...	0.82	0.81	0.82	69	39537	17	4	11	2	16
SRP_00329	Metazoa_SRP links to Rfam database...	0.70	0.69	0.70	59	39819	28	3	22	3	26
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.96	0.94	0.97	34	5425	1	0	1	0	2
SRP_00339	Archaea_SRP links to Rfam database...	0.83	0.82	0.84	77	44459	18	1	14	3	17
SRP_00340	Metazoa_SRP links to Rfam database...	0.70	0.70	0.70	57	41247	26	8	16	2	25

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

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

Total Base Pair Counts
Total TP	1738
Total TN	2789495
Total FP	489
Total FP CONTRA	21
Total FP INCONS	385
Total FP COMP	83
Total FN	3090

Total Scores
MCC	0.540
Average MCC ± 95% Confidence Intervals	0.396 ± 0.065
Sensitivity	0.360
Positive Predictive Value	0.811
Nr of predictions	123

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
CRW_01343	SSU_rRNA_archaea links to Rfam database...	0.64	0.61	0.68	263	977515	145	6	117	22	171
PDB_00005	Tymo_tRNA-like links to Rfam database...	0.53	0.29	1.00	4	942	2	0	0	2	10
PDB_00012	mir-TAR links to Rfam database...	0.65	0.43	1.00	3	403	0	0	0	0	4
PDB_00213	Gammaretro_CES links to Rfam database...	0.73	0.59	0.92	24	5024	2	0	2	0	17
PDB_00553	mir-TAR links to Rfam database...	0.45	0.27	0.75	3	461	1	0	1	0	8
PDB_00716	HDV_ribozyme links to Rfam database...	0.23	0.13	0.43	3	2694	4	0	4	0	20
PDB_00810	s2m links to Rfam database...	0.63	0.53	0.75	9	1069	3	0	3	0	8
PDB_01050	UnaL2 links to Rfam database...	0.55	0.31	1.00	4	626	1	0	0	1	9
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...	0.69	0.48	1.00	25	10128	0	0	0	0	27
PDB_01152	HIV_FS2 links to Rfam database...	0.76	0.64	0.90	9	551	1	0	1	0	5
RFA_00390	Hammerhead_3 links to Rfam database...	0.00	0.00	0.00	0	1431	0	0	0	0	15
RFA_00416	Hammerhead_3 links to Rfam database...	0.00	0.00	0.00	0	1485	0	0	0	0	15
RFA_00433	Hammerhead_3 links to Rfam database...	0.00	0.00	0.00	0	1431	0	0	0	0	15
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...	0.00	0.00	0.00	0	13530	0	0	0	0	35
RFA_00604	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	13530	0	0	0	0	35
RFA_00605	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	15225	0	0	0	0	35
RFA_00606	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	21321	0	0	0	0	39
RFA_00607	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	17766	0	0	0	0	36
RFA_00609	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	17955	0	0	0	0	37
RFA_00610	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	17205	0	0	0	0	37
RFA_00611	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	13041	0	0	0	0	35
RFA_00613	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	12880	0	0	0	0	35
RFA_00615	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	13366	0	0	0	0	35
RFA_00620	Telomerase-cil links to Rfam database...	0.00	0.00	0.00	0	21945	0	0	0	0	39
RFA_00626	rne5 links to Rfam database...	0.81	0.66	1.00	57	56559	4	0	0	4	30
RFA_00627	rne5 links to Rfam database...	0.84	0.70	1.00	61	56892	5	0	0	5	26
RFA_00628	rne5 links to Rfam database...	0.83	0.69	1.00	59	57232	8	0	0	8	27
RFA_00630	rne5 links to Rfam database...	0.82	0.67	1.00	58	56895	4	0	0	4	29
RFA_00632	HDV_ribozyme links to Rfam database...	0.21	0.11	0.43	3	4088	4	0	4	0	25
RFA_00636	HDV_ribozyme links to Rfam database...	0.21	0.11	0.43	3	3998	4	0	4	0	25
RFA_00639	7SK links to Rfam database...	0.21	0.11	0.40	10	54590	15	4	11	0	77
RFA_00642	Vimentin3 links to Rfam database...	0.57	0.44	0.73	8	2915	3	0	3	0	10
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...	0.42	0.33	0.55	6	2690	5	0	5	0	12
RFA_00645	Vimentin3 links to Rfam database...	0.00	0.00	0.00	0	2407	8	0	8	0	18
RFA_00649	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2137	8	0	8	0	18
RFA_00651	Vimentin3 links to Rfam database...	0.42	0.33	0.55	6	2069	5	0	5	0	12
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...	0.57	0.44	0.73	8	2404	3	0	3	0	10
RFA_00658	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1128	0	0	0	0	14
RFA_00659	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1128	0	0	0	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...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00668	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
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...	0.00	0.00	0.00	0	1128	0	0	0	0	14
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...	0.00	0.00	0.00	0	990	0	0	0	0	14
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...	0.00	0.00	0.00	0	1128	0	0	0	0	14
RFA_00684	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00685	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
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...	0.00	0.00	0.00	0	1035	0	0	0	0	14
RFA_00706	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1035	0	0	0	0	14
RFA_00707	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1035	0	0	0	0	14
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...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00710	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	990	0	0	0	0	14
RFA_00711	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	1035	0	0	0	0	14
RFA_00715	Hammerhead_1 links to Rfam database...	0.00	0.00	0.00	0	946	0	0	0	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...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00731	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00733	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00734	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00736	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00737	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00745	s2m links to Rfam database...	1.00	1.00	1.00	12	934	0	0	0	0	0
RFA_00749	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00758	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00762	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00763	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00764	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00765	s2m links to Rfam database...	1.00	1.00	1.00	12	891	0	0	0	0	0
RFA_00767	Corona_pk3 links to Rfam database...	0.47	0.33	0.67	6	1882	3	0	3	0	12
RFA_00768	Corona_pk3 links to Rfam database...	0.41	0.28	0.63	5	1883	3	0	3	0	13
RFA_00769	Corona_pk3 links to Rfam database...	0.57	0.44	0.73	8	1942	3	0	3	0	10
RFA_00770	Corona_pk3 links to Rfam database...	0.57	0.44	0.73	8	2005	3	0	3	0	10
RFA_00773	Corona_pk3 links to Rfam database...	0.41	0.28	0.63	5	1945	3	0	3	0	13
RFA_00779	Corona_pk3 links to Rfam database...	0.47	0.33	0.67	6	1944	3	0	3	0	12
RFA_00781	Gammaretro_CES links to Rfam database...	0.83	0.75	0.92	24	5024	2	0	2	0	8
RFA_00786	Gammaretro_CES links to Rfam database...	0.83	0.75	0.92	24	5024	2	0	2	0	8
RFA_00791	Gammaretro_CES links to Rfam database...	0.83	0.75	0.92	24	5125	2	0	2	0	8
RFA_00792	Gammaretro_CES links to Rfam database...	0.83	0.75	0.92	24	5024	2	0	2	0	8
RFA_00801	Gammaretro_CES links to Rfam database...	0.80	0.72	0.88	23	5024	3	0	3	0	9
RFA_00808	RydC links to Rfam database...	0.75	0.56	1.00	9	2007	0	0	0	0	7
RFA_00809	RydC links to Rfam database...	0.50	0.38	0.67	6	2136	3	0	3	0	10
RFA_00814	R2_retro_el links to Rfam database...	0.75	0.63	0.90	26	25171	4	0	3	1	15
RFA_00815	R2_retro_el links to Rfam database...	0.83	0.68	1.00	28	24503	1	0	0	1	13
RFA_00816	R2_retro_el links to Rfam database...	0.75	0.63	0.90	26	23191	4	0	3	1	15
RFA_00817	R2_retro_el links to Rfam database...	0.83	0.68	1.00	28	21917	1	0	0	1	13
RFA_00818	R2_retro_el links to Rfam database...	0.83	0.68	1.00	28	20273	1	0	0	1	13
RFA_00819	R2_retro_el links to Rfam database...	0.83	0.68	1.00	28	27938	0	0	0	0	13
RFA_00820	bicoid_3 links to Rfam database...	0.71	0.56	0.89	90	151424	13	3	8	2	70
RFA_00830	bicoid_3 links to Rfam database...	0.59	0.45	0.78	70	152538	23	3	17	3	84
SRP_00079	Plant_SRP links to Rfam database...	0.54	0.33	0.88	29	41872	6	0	4	2	59
SRP_00124	Metazoa_SRP links to Rfam database...	0.15	0.09	0.24	8	37094	27	3	23	1	77
SRP_00137	Bacteria_small_SRP links to Rfam database...	0.49	0.24	1.00	6	4180	0	0	0	0	19
SRP_00141	Bacteria_small_SRP links to Rfam database...	0.35	0.12	1.00	5	6323	1	0	0	1	36
SRP_00146	Bacteria_small_SRP links to Rfam database...	0.41	0.17	1.00	6	5247	0	0	0	0	30
SRP_00182	Plant_SRP links to Rfam database...	0.59	0.35	1.00	35	46021	1	0	0	1	66
SRP_00197	Archaea_SRP links to Rfam database...	0.47	0.28	0.80	28	49420	8	0	7	1	73
SRP_00198	Archaea_SRP links to Rfam database...	0.47	0.27	0.82	28	51006	7	0	6	1	75
SRP_00199	Archaea_SRP links to Rfam database...	0.47	0.24	0.93	25	51013	3	0	2	1	80
SRP_00202	Archaea_SRP links to Rfam database...	0.48	0.25	0.94	29	54254	2	0	2	0	88
SRP_00241	Plant_SRP links to Rfam database...	0.51	0.33	0.79	27	46022	9	0	7	2	55
SRP_00255	Archaea_SRP links to Rfam database...	0.65	0.43	1.00	40	47546	2	0	0	2	54
SRP_00260	Metazoa_SRP links to Rfam database...	0.21	0.14	0.33	14	47852	29	1	28	0	86
SRP_00278	Archaea_SRP links to Rfam database...	0.53	0.30	0.94	31	46023	3	0	2	1	74
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.45	0.20	1.00	6	3735	0	0	0	0	24
SRP_00322	Archaea_SRP links to Rfam database...	0.44	0.25	0.79	27	48482	8	0	7	1	82
SRP_00328	Metazoa_SRP links to Rfam database...	0.49	0.34	0.71	29	39580	16	1	11	4	56
SRP_00329	Metazoa_SRP links to Rfam database...	0.50	0.34	0.73	29	39863	16	0	11	5	56
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.41	0.17	1.00	6	5454	0	0	0	0	30
SRP_00339	Archaea_SRP links to Rfam database...	0.49	0.32	0.77	30	44512	9	0	9	0	64
SRP_00340	Metazoa_SRP links to Rfam database...	0.44	0.27	0.73	22	41298	12	0	8	4	60

^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 ContextFold - scored higher in this pairwise comparison

1. Total counts & total scores for ContextFold

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

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

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

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