CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	UNAFold		Murlet(seed)
MCC	0.600	>	0.540
Average MCC ± 95% Confidence Intervals	0.591 ± 0.053	>	0.396 ± 0.065
Sensitivity	0.593	>	0.360
Positive Predictive Value	0.609	<	0.811
Total TP	2862	>	1738
Total TN	2786939	<	2789495
Total FP	2292	>	489
Total FP CONTRA	334	>	21
Total FP INCONS	1504	>	385
Total FP COMP	454	>	83
Total FN	1966	<	3090
P-value	3.56938820447e-08

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Performance plots

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

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Performance of UNAFold - scored higher in this pairwise comparison

1. Total counts & total scores for UNAFold

Total Base Pair Counts
Total TP	2862
Total TN	2786939
Total FP	2292
Total FP CONTRA	334
Total FP INCONS	1504
Total FP COMP	454
Total FN	1966

Total Scores
MCC	0.600
Average MCC ± 95% Confidence Intervals	0.591 ± 0.053
Sensitivity	0.593
Positive Predictive Value	0.609
Nr of predictions	123

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2. Individual counts for UNAFold [ 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...	0.35	0.35	0.35	151	977475	287	44	231	12	283
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	2677	24	5	19	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...	0.92	0.85	1.00	11	619	2	0	0	2	2
PDB_01051	Telomerase-cil links to Rfam database...	0.88	0.85	0.92	11	891	5	0	1	4	2
PDB_01092	glmS links to Rfam database...	0.74	0.65	0.83	34	10112	8	1	6	1	18
PDB_01152	HIV_FS2 links to Rfam database...	0.92	0.86	1.00	12	549	0	0	0	0	2
RFA_00390	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1416	2	0	0	2	0
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_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...	0.69	0.74	0.63	26	13489	18	4	11	3	9
RFA_00604	Telomerase-cil links to Rfam database...	0.70	0.71	0.69	25	13494	22	2	9	11	10
RFA_00605	Telomerase-cil links to Rfam database...	0.37	0.34	0.40	12	15195	27	3	15	9	23
RFA_00606	Telomerase-cil links to Rfam database...	0.67	0.67	0.68	26	21283	25	7	5	13	13
RFA_00607	Telomerase-cil links to Rfam database...	0.83	0.83	0.83	30	17730	18	4	2	12	6
RFA_00609	Telomerase-cil links to Rfam database...	0.75	0.76	0.74	28	17917	27	2	8	17	9
RFA_00610	Telomerase-cil links to Rfam database...	0.77	0.76	0.78	28	17169	23	2	6	15	9
RFA_00611	Telomerase-cil links to Rfam database...	0.84	0.83	0.85	29	13007	10	0	5	5	6
RFA_00613	Telomerase-cil links to Rfam database...	0.66	0.66	0.66	23	12845	15	4	8	3	12
RFA_00615	Telomerase-cil links to Rfam database...	0.65	0.69	0.62	24	13327	15	4	11	0	11
RFA_00620	Telomerase-cil links to Rfam database...	0.67	0.64	0.69	25	21909	24	3	8	13	14
RFA_00626	rne5 links to Rfam database...	0.87	0.84	0.91	73	56536	32	2	5	25	14
RFA_00627	rne5 links to Rfam database...	0.70	0.67	0.74	58	56875	36	4	16	16	29
RFA_00628	rne5 links to Rfam database...	0.86	0.83	0.89	71	57211	31	1	8	22	15
RFA_00630	rne5 links to Rfam database...	0.59	0.59	0.59	51	56866	48	8	28	12	36
RFA_00632	HDV_ribozyme links to Rfam database...	0.34	0.36	0.33	10	4065	20	2	18	0	18
RFA_00636	HDV_ribozyme links to Rfam database...	0.43	0.43	0.44	12	3978	15	2	13	0	16
RFA_00639	7SK links to Rfam database...	0.17	0.18	0.16	16	54518	83	18	63	2	71
RFA_00642	Vimentin3 links to Rfam database...	0.25	0.22	0.29	4	2912	10	2	8	0	14
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...	-0.01	0.00	0.00	0	2681	20	4	16	0	18
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...	0.68	0.67	0.71	12	2128	7	1	4	2	6
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...	0.33	0.33	0.33	6	2127	12	3	9	0	12
RFA_00654	Vimentin3 links to Rfam database...	0.27	0.28	0.28	5	2397	13	2	11	0	13
RFA_00658	Hammerhead_1 links to Rfam database...	0.59	0.50	0.70	7	1118	5	0	3	2	7
RFA_00659	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1120	10	1	7	2	14
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	8	1	7	0	10
RFA_00668	Hammerhead_1 links to Rfam database...	0.41	0.43	0.40	6	975	9	0	9	0	8
RFA_00672	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	895	9	0	8	1	13
RFA_00673	Hammerhead_1 links to Rfam database...	0.42	0.36	0.50	5	1118	6	0	5	1	9
RFA_00674	Hammerhead_1 links to Rfam database...	0.71	0.71	0.71	10	1114	5	0	4	1	4
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...	0.42	0.43	0.43	6	976	9	0	8	1	8
RFA_00678	Hammerhead_1 links to Rfam database...	0.43	0.29	0.67	4	940	2	0	2	0	10
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...	0.66	0.64	0.69	9	977	5	0	4	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...	0.56	0.50	0.64	7	7010	29	1	3	25	7
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...	0.32	0.21	0.50	3	984	4	0	3	1	11
RFA_00705	Hammerhead_1 links to Rfam database...	0.69	0.71	0.67	10	1020	5	0	5	0	4
RFA_00706	Hammerhead_1 links to Rfam database...	0.37	0.29	0.50	4	1027	4	0	4	0	10
RFA_00707	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	1026	9	3	6	0	14
RFA_00708	Hammerhead_1 links to Rfam database...	0.40	0.29	0.57	4	1028	3	0	3	0	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	981	9	0	9	0	14
RFA_00711	Hammerhead_1 links to Rfam database...	0.33	0.29	0.40	4	1025	6	0	6	0	10
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	935	11	0	11	0	14
RFA_00717	Hammerhead_1 links to Rfam database...	0.64	0.64	0.64	9	889	5	0	5	0	5
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...	0.69	0.67	0.73	8	892	4	1	2	1	4
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...	0.69	0.67	0.73	8	892	4	1	2	1	4
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...	0.69	0.67	0.73	8	892	4	1	2	1	4
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...	0.64	0.67	0.62	8	890	5	1	4	0	4
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...	0.69	0.67	0.73	8	892	4	1	2	1	4
RFA_00765	s2m links to Rfam database...	1.00	1.00	1.00	12	891	1	0	0	1	0
RFA_00767	Corona_pk3 links to Rfam database...	0.63	0.56	0.71	10	1877	4	0	4	0	8
RFA_00768	Corona_pk3 links to Rfam database...	0.48	0.44	0.53	8	1876	7	1	6	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...	0.61	0.56	0.67	10	2001	8	0	5	3	8
RFA_00773	Corona_pk3 links to Rfam database...	0.71	0.56	0.91	10	1942	4	1	0	3	8
RFA_00779	Corona_pk3 links to Rfam database...	0.55	0.56	0.56	10	1935	8	3	5	0	8
RFA_00781	Gammaretro_CES links to Rfam database...	0.58	0.59	0.58	19	5017	14	2	12	0	13
RFA_00786	Gammaretro_CES links to Rfam database...	0.71	0.72	0.70	23	5017	10	2	8	0	9
RFA_00791	Gammaretro_CES links to Rfam database...	0.95	0.91	1.00	29	5122	1	0	0	1	3
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...	0.85	0.81	0.90	26	5021	4	0	3	1	6
RFA_00808	RydC links to Rfam database...	-0.01	0.00	0.00	0	2001	15	2	13	0	16
RFA_00809	RydC links to Rfam database...	0.37	0.38	0.38	6	2129	10	1	9	0	10
RFA_00814	R2_retro_el links to Rfam database...	0.77	0.78	0.76	32	25158	23	4	6	13	9
RFA_00815	R2_retro_el links to Rfam database...	0.56	0.61	0.51	25	24482	36	8	16	12	16
RFA_00816	R2_retro_el links to Rfam database...	0.60	0.66	0.55	27	23171	30	13	9	8	14
RFA_00817	R2_retro_el links to Rfam database...	0.10	0.12	0.08	5	21882	58	18	40	0	36
RFA_00818	R2_retro_el links to Rfam database...	0.19	0.22	0.17	9	20247	46	19	26	1	32
RFA_00819	R2_retro_el links to Rfam database...	0.96	0.95	0.98	39	27926	28	0	1	27	2
RFA_00820	bicoid_3 links to Rfam database...	0.89	0.90	0.88	144	151362	33	2	17	14	16
RFA_00830	bicoid_3 links to Rfam database...	0.48	0.45	0.52	70	152493	109	5	60	44	84
SRP_00079	Plant_SRP links to Rfam database...	0.50	0.52	0.49	46	41811	53	7	41	5	42
SRP_00124	Metazoa_SRP links to Rfam database...	0.54	0.52	0.56	44	37049	37	5	30	2	41
SRP_00137	Bacteria_small_SRP links to Rfam database...	0.74	0.84	0.66	21	4154	13	4	7	2	4
SRP_00141	Bacteria_small_SRP links to Rfam database...	0.91	0.90	0.93	37	6288	3	1	2	0	4
SRP_00146	Bacteria_small_SRP links to Rfam database...	0.93	0.94	0.92	34	5216	3	1	2	0	2
SRP_00182	Plant_SRP links to Rfam database...	0.70	0.68	0.73	69	45961	27	5	21	1	32
SRP_00197	Archaea_SRP links to Rfam database...	0.44	0.43	0.45	43	49360	53	4	48	1	58
SRP_00198	Archaea_SRP links to Rfam database...	0.34	0.34	0.35	35	50940	66	4	61	1	68
SRP_00199	Archaea_SRP links to Rfam database...	0.65	0.65	0.66	68	50937	36	3	32	1	37
SRP_00202	Archaea_SRP links to Rfam database...	0.97	0.95	0.98	111	54172	4	0	2	2	6
SRP_00241	Plant_SRP links to Rfam database...	0.48	0.51	0.45	42	45963	53	14	37	2	40
SRP_00255	Archaea_SRP links to Rfam database...	0.60	0.62	0.59	58	47487	46	3	38	5	36
SRP_00260	Metazoa_SRP links to Rfam database...	0.73	0.74	0.73	74	47793	30	8	20	2	26
SRP_00278	Archaea_SRP links to Rfam database...	0.77	0.76	0.78	80	45954	23	5	17	1	25
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.98	0.97	1.00	29	3712	0	0	0	0	1
SRP_00322	Archaea_SRP links to Rfam database...	0.61	0.61	0.60	67	48405	45	6	38	1	42
SRP_00328	Metazoa_SRP links to Rfam database...	0.64	0.65	0.63	55	39534	37	7	25	5	30
SRP_00329	Metazoa_SRP links to Rfam database...	0.74	0.73	0.75	62	39820	24	3	18	3	23
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.97	0.97	0.97	35	5424	1	0	1	0	1
SRP_00339	Archaea_SRP links to Rfam database...	0.64	0.64	0.64	60	44457	37	6	28	3	34
SRP_00340	Metazoa_SRP links to Rfam database...	0.54	0.57	0.52	47	41237	46	8	36	2	35

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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 UNAFold - scored higher in this pairwise comparison

1. Total counts & total scores for UNAFold

2. Individual counts for UNAFold [ 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 ]