CompaRNA - on-line benchmarks of RNA structure prediction methods

Laboratory of Structural Bioinformatics @ Adam Mickiewicz University in Poznan

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Overview

Metric	CentroidAlifold(seed)		IPknot
MCC	0.790	>	0.733
Average MCC ± 95% Confidence Intervals	0.776 ± 0.028	>	0.704 ± 0.039
Sensitivity	0.699	<	0.708
Positive Predictive Value	0.896	>	0.762
Total TP	3572	<	3617
Total TN	854811	>	854050
Total FP	757	<	1484
Total FP CONTRA	59	<	164
Total FP INCONS	354	<	965
Total FP COMP	344	<	355
Total FN	1538	>	1493
P-value	3.56938820447e-08

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Performance plots

Comparison of performance of CentroidAlifold(seed) and IPknot. 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 CentroidAlifold(seed) and IPknot).
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 CentroidAlifold(seed) and IPknot).
Comparison of average Matthews Correlation Coefficients (MCCs) for CentroidAlifold(seed) and IPknot. 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 CentroidAlifold(seed) and IPknot).

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

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

Total Base Pair Counts
Total TP	3572
Total TN	854811
Total FP	757
Total FP CONTRA	59
Total FP INCONS	354
Total FP COMP	344
Total FN	1538

Total Scores
MCC	0.790
Average MCC ± 95% Confidence Intervals	0.776 ± 0.028
Sensitivity	0.699
Positive Predictive Value	0.896
Nr of predictions	216

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
ASE_00251	RNaseP_nuc links to Rfam database...	0.68	0.51	0.92	22	17742	13	0	2	11	21
PDB_00005	Tymo_tRNA-like links to Rfam database...	0.80	0.64	1.00	9	937	0	0	0	0	5
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...	0.95	0.91	1.00	10	455	0	0	0	0	1
PDB_00716	HDV_ribozyme links to Rfam database...	0.75	0.61	0.93	14	2686	1	0	1	0	9
PDB_00741	Entero_5_CRE links to Rfam database...	0.72	0.53	1.00	9	694	0	0	0	0	8
PDB_00810	s2m links to Rfam database...	0.87	0.76	1.00	13	1068	1	0	0	1	4
PDB_00828	Purine links to Rfam database...	0.88	0.78	1.00	21	2464	0	0	0	0	6
PDB_00829	Purine links to Rfam database...	0.91	0.83	1.00	20	2258	0	0	0	0	4
PDB_00876	HIV_FE links to Rfam database...	0.53	0.50	0.59	10	973	7	0	7	0	10
PDB_01001	tRNA links to Rfam database...	0.00	0.00	0.00	0	2139	6	0	6	0	18
PDB_01020	Purine links to Rfam database...	0.91	0.83	1.00	19	2259	1	0	0	1	4
PDB_01050	UnaL2 links to Rfam database...	0.68	0.46	1.00	6	624	2	0	0	2	7
PDB_01051	Telomerase-cil links to Rfam database...	0.96	0.92	1.00	12	891	4	0	0	4	1
PDB_01073	SAM links to Rfam database...	0.84	0.71	1.00	24	4347	1	0	0	1	10
PDB_01092	glmS links to Rfam database...	0.72	0.58	0.91	30	10120	4	0	3	1	22
PDB_01114	TPP links to Rfam database...	0.77	0.59	1.00	16	2834	1	0	0	1	11
PDB_01152	HIV_FS2 links to Rfam database...	0.80	0.64	1.00	9	552	0	0	0	0	5
PDB_01236	ykoK links to Rfam database...	0.88	0.78	1.00	42	11586	3	0	0	3	12
RFA_00389	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	3	0	0	3	1
RFA_00390	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	2	0	0	2	1
RFA_00391	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	3	0	0	3	1
RFA_00396	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	3	0	0	3	1
RFA_00402	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	3	0	0	3	1
RFA_00409	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	3	0	0	3	1
RFA_00416	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1471	2	0	0	2	1
RFA_00425	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1639	3	0	0	3	1
RFA_00427	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1471	3	0	0	3	1
RFA_00433	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	2	0	0	2	1
RFA_00434	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	3	0	0	3	1
RFA_00436	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	3	0	0	3	1
RFA_00440	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1471	3	0	0	3	1
RFA_00442	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	3	0	0	3	1
RFA_00444	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1526	3	0	0	3	1
RFA_00446	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1471	3	0	0	3	1
RFA_00449	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1471	3	0	0	3	1
RFA_00582	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	5980	3	0	0	3	0
RFA_00583	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4935	3	0	0	3	0
RFA_00584	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	2911	3	0	0	3	0
RFA_00585	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	3	0	0	3	0
RFA_00586	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	3901	3	0	0	3	0
RFA_00587	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	3	0	0	3	0
RFA_00588	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4545	3	0	0	3	0
RFA_00589	Y_RNA links to Rfam database...	0.97	0.93	1.00	14	4357	3	0	0	3	1
RFA_00594	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	2760	3	0	0	3	0
RFA_00596	Y_RNA links to Rfam database...	0.93	0.87	1.00	13	5982	3	0	0	3	2
RFA_00603	Telomerase-cil links to Rfam database...	0.96	0.91	1.00	32	13498	0	0	0	0	3
RFA_00604	Telomerase-cil links to Rfam database...	0.97	0.94	1.00	33	13497	0	0	0	0	2
RFA_00605	Telomerase-cil links to Rfam database...	0.97	0.94	1.00	33	15192	0	0	0	0	2
RFA_00607	Telomerase-cil links to Rfam database...	0.94	0.89	1.00	32	17734	0	0	0	0	4
RFA_00609	Telomerase-cil links to Rfam database...	0.93	0.86	1.00	32	17923	0	0	0	0	5
RFA_00610	Telomerase-cil links to Rfam database...	0.93	0.86	1.00	32	17173	0	0	0	0	5
RFA_00611	Telomerase-cil links to Rfam database...	0.96	0.91	1.00	32	13009	0	0	0	0	3
RFA_00613	Telomerase-cil links to Rfam database...	0.97	0.94	1.00	33	12847	0	0	0	0	2
RFA_00615	Telomerase-cil links to Rfam database...	0.85	0.80	0.90	28	13335	3	0	3	0	7
RFA_00632	HDV_ribozyme links to Rfam database...	0.74	0.64	0.86	18	4074	3	2	1	0	10
RFA_00636	HDV_ribozyme links to Rfam database...	0.78	0.68	0.90	19	3984	2	2	0	0	9
RFA_00642	Vimentin3 links to Rfam database...	0.41	0.17	1.00	3	2923	0	0	0	0	15
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...	0.23	0.06	1.00	1	2414	0	0	0	0	17
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...	0.33	0.11	1.00	2	2143	0	0	0	0	16
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...	0.71	0.57	0.89	8	1119	2	0	1	1	6
RFA_00659	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	1122	0	0	0	0	8
RFA_00664	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	984	0	0	0	0	8
RFA_00667	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	984	0	0	0	0	8
RFA_00668	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	984	0	0	0	0	8
RFA_00672	Hammerhead_1 links to Rfam database...	0.78	0.62	1.00	8	895	0	0	0	0	5
RFA_00673	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	1122	0	0	0	0	8
RFA_00674	Hammerhead_1 links to Rfam database...	0.60	0.43	0.86	6	1121	1	0	1	0	8
RFA_00675	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	984	0	0	0	0	8
RFA_00677	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	984	0	0	0	0	8
RFA_00678	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	940	0	0	0	0	8
RFA_00680	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	1122	0	0	0	0	8
RFA_00684	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	984	0	0	0	0	8
RFA_00685	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	984	0	0	0	0	8
RFA_00695	Hammerhead_1 links to Rfam database...	0.80	0.64	1.00	9	7012	0	0	0	0	5
RFA_00703	Hammerhead_1 links to Rfam database...	0.80	0.64	1.00	9	4269	0	0	0	0	5
RFA_00704	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	984	0	0	0	0	8
RFA_00705	Hammerhead_1 links to Rfam database...	0.76	0.64	0.90	9	1025	2	0	1	1	5
RFA_00706	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	1029	0	0	0	0	8
RFA_00707	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	1029	0	0	0	0	8
RFA_00708	Hammerhead_1 links to Rfam database...	0.71	0.57	0.89	8	1026	2	0	1	1	6
RFA_00709	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	984	0	0	0	0	8
RFA_00710	Hammerhead_1 links to Rfam database...	0.72	0.64	0.82	9	979	3	0	2	1	5
RFA_00711	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	1029	0	0	0	0	8
RFA_00715	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	940	0	0	0	0	8
RFA_00716	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	940	0	0	0	0	8
RFA_00717	Hammerhead_1 links to Rfam database...	0.75	0.57	1.00	8	895	0	0	0	0	6
RFA_00730	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00731	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00733	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00734	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00736	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00737	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00745	s2m links to Rfam database...	1.00	1.00	1.00	12	934	2	0	0	2	0
RFA_00749	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00758	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00762	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00763	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00764	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
RFA_00765	s2m links to Rfam database...	1.00	1.00	1.00	12	891	2	0	0	2	0
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...	0.74	0.56	1.00	10	1943	0	0	0	0	8
RFA_00770	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	2006	0	0	0	0	8
RFA_00773	Corona_pk3 links to Rfam database...	0.74	0.56	1.00	10	1943	0	0	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...	0.97	0.94	1.00	30	5020	0	0	0	0	2
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...	0.97	0.94	1.00	30	5121	0	0	0	0	2
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...	0.97	0.94	1.00	30	5020	0	0	0	0	2
RFA_00808	RydC links to Rfam database...	0.65	0.56	0.75	9	2004	3	1	2	0	7
RFA_00809	RydC links to Rfam database...	0.43	0.38	0.50	6	2133	6	0	6	0	10
SPR_00020	tRNA links to Rfam database...	0.55	0.30	1.00	6	2695	0	0	0	0	14
SPR_00023	tRNA links to Rfam database...	0.53	0.29	1.00	6	2844	0	0	0	0	15
SPR_00137	tRNA links to Rfam database...	0.49	0.24	1.00	5	2921	1	0	0	1	16
SPR_00273	tRNA links to Rfam database...	0.44	0.24	0.83	5	2844	1	0	1	0	16
SPR_00277	tRNA links to Rfam database...	0.53	0.29	1.00	6	2920	0	0	0	0	15
SPR_00394	tRNA links to Rfam database...	0.53	0.29	1.00	6	3649	0	0	0	0	15
SPR_00402	tRNA links to Rfam database...	0.53	0.29	1.00	6	2550	0	0	0	0	15
SPR_00721	tRNA links to Rfam database...	0.53	0.29	1.00	6	2920	0	0	0	0	15
SPR_00816	tRNA links to Rfam database...	0.55	0.30	1.00	6	3480	0	0	0	0	14
SPR_01157	tRNA links to Rfam database...	0.53	0.29	1.00	6	2769	0	0	0	0	15
SRP_00001	Bacteria_large_SRP links to Rfam database...	0.82	0.68	1.00	27	6759	5	0	0	5	13
SRP_00008	Bacteria_small_SRP links to Rfam database...	0.96	0.92	1.00	23	2903	2	0	0	2	2
SRP_00020	Bacteria_small_SRP links to Rfam database...	0.89	0.85	0.93	28	5535	2	1	1	0	5
SRP_00038	Bacteria_small_SRP links to Rfam database...	0.90	0.82	1.00	27	5023	3	0	0	3	6
SRP_00040	Bacteria_small_SRP links to Rfam database...	0.55	0.52	0.59	16	5538	14	1	10	3	15
SRP_00042	Bacteria_small_SRP links to Rfam database...	0.85	0.80	0.91	20	3983	6	1	1	4	5
SRP_00043	Bacteria_small_SRP links to Rfam database...	0.42	0.41	0.43	12	5022	18	2	14	2	17
SRP_00044	Bacteria_small_SRP links to Rfam database...	0.85	0.81	0.90	26	6076	4	1	2	1	6
SRP_00046	Bacteria_small_SRP links to Rfam database...	0.94	0.88	1.00	28	4725	2	0	0	2	4
SRP_00051	Bacteria_small_SRP links to Rfam database...	0.76	0.67	0.87	20	5437	7	0	3	4	10
SRP_00054	Bacteria_small_SRP links to Rfam database...	0.92	0.84	1.00	27	5538	3	0	0	3	5
SRP_00056	Bacteria_small_SRP links to Rfam database...	0.63	0.54	0.74	20	6414	9	1	6	2	17
SRP_00057	Bacteria_small_SRP links to Rfam database...	0.79	0.69	0.92	24	6302	6	1	1	4	11
SRP_00058	Bacteria_small_SRP links to Rfam database...	0.88	0.82	0.93	28	5748	2	1	1	0	6
SRP_00067	Bacteria_small_SRP links to Rfam database...	0.81	0.71	0.93	27	5749	3	1	1	1	11
SRP_00072	Bacteria_small_SRP links to Rfam database...	0.68	0.66	0.70	19	6301	11	0	8	3	10
SRP_00074	Bacteria_small_SRP links to Rfam database...	0.52	0.48	0.56	14	6530	16	0	11	5	15
SRP_00075	Bacteria_small_SRP links to Rfam database...	0.34	0.32	0.37	11	5535	19	0	19	0	23
SRP_00077	Bacteria_small_SRP links to Rfam database...	0.59	0.51	0.68	19	6642	11	0	9	2	18
SRP_00081	Bacteria_small_SRP links to Rfam database...	0.65	0.65	0.67	20	5535	10	1	9	0	11
SRP_00084	Bacteria_small_SRP links to Rfam database...	0.88	0.82	0.93	28	5430	2	1	1	0	6
SRP_00094	Bacteria_small_SRP links to Rfam database...	0.82	0.83	0.80	20	4070	9	1	4	4	4
SRP_00095	Bacteria_small_SRP links to Rfam database...	0.82	0.84	0.81	21	3979	8	1	4	3	4
SRP_00098	Bacteria_small_SRP links to Rfam database...	0.65	0.57	0.75	21	6413	9	1	6	2	16
SRP_00105	Bacteria_small_SRP links to Rfam database...	0.89	0.79	1.00	27	5538	3	0	0	3	7
SRP_00106	Bacteria_large_SRP links to Rfam database...	0.69	0.72	0.67	18	5226	15	3	6	6	7
SRP_00107	Bacteria_small_SRP links to Rfam database...	0.46	0.53	0.40	10	3630	19	3	12	4	9
SRP_00121	Bacteria_small_SRP links to Rfam database...	0.82	0.80	0.83	20	4254	6	0	4	2	5
SRP_00128	Bacteria_small_SRP links to Rfam database...	0.82	0.72	0.93	26	6758	4	1	1	2	10
SRP_00132	Bacteria_small_SRP links to Rfam database...	0.73	0.69	0.77	20	4825	9	0	6	3	9
SRP_00134	Bacteria_large_SRP links to Rfam database...	0.70	0.62	0.78	18	5972	13	0	5	8	11
SRP_00137	Bacteria_small_SRP links to Rfam database...	0.66	0.68	0.65	17	4160	10	3	6	1	8
SRP_00141	Bacteria_small_SRP links to Rfam database...	0.78	0.66	0.93	27	6299	3	1	1	1	14
SRP_00145	Bacteria_small_SRP links to Rfam database...	0.81	0.70	0.93	28	6298	2	1	1	0	12
SRP_00146	Bacteria_small_SRP links to Rfam database...	0.83	0.75	0.93	27	5224	3	1	1	1	9
SRP_00161	Bacteria_small_SRP links to Rfam database...	0.84	0.82	0.86	18	2829	5	0	3	2	4
SRP_00162	Bacteria_small_SRP links to Rfam database...	0.87	0.87	0.87	20	2903	4	0	3	1	3
SRP_00163	Bacteria_small_SRP links to Rfam database...	0.84	0.81	0.88	21	3462	5	0	3	2	5
SRP_00164	Bacteria_small_SRP links to Rfam database...	0.78	0.66	0.92	23	6878	7	1	1	5	12
SRP_00170	Bacteria_small_SRP links to Rfam database...	0.83	0.76	0.90	19	4074	6	1	1	4	6
SRP_00194	Bacteria_small_SRP links to Rfam database...	0.71	0.71	0.71	15	3219	9	0	6	3	6
SRP_00200	Bacteria_small_SRP links to Rfam database...	0.77	0.67	0.89	24	6876	6	1	2	3	12
SRP_00209	Bacteria_small_SRP links to Rfam database...	0.75	0.74	0.77	20	4630	9	1	5	3	7
SRP_00213	Bacteria_small_SRP links to Rfam database...	0.92	0.92	0.92	23	4161	6	1	1	4	2
SRP_00215	Bacteria_small_SRP links to Rfam database...	0.86	0.84	0.88	21	3216	4	0	3	1	4
SRP_00216	Bacteria_small_SRP links to Rfam database...	0.93	0.93	0.93	25	3376	4	1	1	2	2
SRP_00217	Bacteria_small_SRP links to Rfam database...	0.89	0.88	0.91	21	3298	4	0	2	2	3
SRP_00219	Bacteria_small_SRP links to Rfam database...	0.89	0.87	0.91	20	3299	5	0	2	3	3
SRP_00222	Bacteria_small_SRP links to Rfam database...	0.87	0.84	0.91	21	3058	3	1	1	1	4
SRP_00227	Bacteria_small_SRP links to Rfam database...	0.86	0.81	0.93	25	5124	5	1	1	3	6
SRP_00229	Bacteria_small_SRP links to Rfam database...	0.41	0.41	0.42	11	5227	19	0	15	4	16
SRP_00231	Bacteria_small_SRP links to Rfam database...	0.88	0.82	0.93	28	5430	2	1	1	0	6
SRP_00233	Bacteria_small_SRP links to Rfam database...	0.87	0.82	0.93	27	5122	3	0	2	1	6
SRP_00243	Bacteria_small_SRP links to Rfam database...	0.88	0.81	0.96	25	5125	5	0	1	4	6
SRP_00244	Bacteria_small_SRP links to Rfam database...	0.74	0.62	0.89	24	6876	5	1	2	2	15
SRP_00250	Bacteria_small_SRP links to Rfam database...	0.67	0.58	0.78	21	6759	9	1	5	3	15
SRP_00251	Bacteria_small_SRP links to Rfam database...	0.77	0.67	0.89	24	6994	6	1	2	3	12
SRP_00266	Bacteria_small_SRP links to Rfam database...	0.55	0.55	0.55	16	4627	14	2	11	1	13
SRP_00268	Bacteria_small_SRP links to Rfam database...	0.91	0.89	0.92	24	4160	5	1	1	3	3
SRP_00269	Bacteria_small_SRP links to Rfam database...	0.68	0.64	0.72	21	5021	9	0	8	1	12
SRP_00270	Bacteria_small_SRP links to Rfam database...	0.86	0.81	0.93	25	4629	5	0	2	3	6
SRP_00271	Bacteria_small_SRP links to Rfam database...	0.89	0.88	0.91	21	3217	3	0	2	1	3
SRP_00273	Bacteria_small_SRP links to Rfam database...	0.79	0.68	0.93	27	6757	3	1	1	1	13
SRP_00274	Bacteria_small_SRP links to Rfam database...	0.81	0.71	0.93	27	6874	3	1	1	1	11
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.87	0.77	1.00	23	3718	2	0	0	2	7
SRP_00295	Bacteria_small_SRP links to Rfam database...	0.78	0.66	0.93	25	6876	5	1	1	3	13
SRP_00303	Bacteria_small_SRP links to Rfam database...	0.68	0.63	0.74	20	6643	10	1	6	3	12
SRP_00310	Bacteria_small_SRP links to Rfam database...	0.82	0.83	0.83	19	2903	5	0	4	1	4
SRP_00312	Bacteria_small_SRP links to Rfam database...	0.91	0.89	0.92	24	4160	5	1	1	3	3
SRP_00315	Bacteria_small_SRP links to Rfam database...	0.81	0.83	0.79	19	2902	5	0	5	0	4
SRP_00318	Bacteria_small_SRP links to Rfam database...	0.81	0.83	0.79	19	2979	5	0	5	0	4
SRP_00324	Bacteria_small_SRP links to Rfam database...	0.62	0.59	0.65	17	5330	10	1	8	1	12
SRP_00325	Bacteria_small_SRP links to Rfam database...	0.87	0.82	0.93	27	4342	3	0	2	1	6
SRP_00326	Bacteria_small_SRP links to Rfam database...	0.86	0.81	0.93	25	5023	5	0	2	3	6
SRP_00333	Bacteria_small_SRP links to Rfam database...	0.86	0.79	0.93	27	5122	3	0	2	1	7
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.90	0.81	1.00	29	5431	1	0	0	1	7
SRP_00341	Bacteria_small_SRP links to Rfam database...	0.44	0.42	0.46	13	4725	17	0	15	2	18
SRP_00342	Bacteria_small_SRP links to Rfam database...	0.72	0.72	0.72	18	3980	12	0	7	5	7
SRP_00350	Bacteria_small_SRP links to Rfam database...	0.84	0.78	0.91	21	3893	4	1	1	2	6
SRP_00356	Bacteria_small_SRP links to Rfam database...	0.80	0.73	0.88	22	5025	6	0	3	3	8
SRP_00357	Bacteria_small_SRP links to Rfam database...	0.82	0.72	0.93	26	5328	4	1	1	2	10
SRP_00358	Bacteria_small_SRP links to Rfam database...	0.81	0.71	0.93	25	6301	5	1	1	3	10
SRP_00363	Bacteria_small_SRP links to Rfam database...	0.82	0.77	0.88	23	4727	7	0	3	4	7
SRP_00365	Bacteria_small_SRP links to Rfam database...	0.84	0.78	0.91	21	3380	4	0	2	2	6
SRP_00367	Bacteria_small_SRP links to Rfam database...	0.79	0.69	0.92	24	6760	6	1	1	4	11
SRP_00369	Bacteria_small_SRP links to Rfam database...	0.78	0.66	0.92	23	5753	7	1	1	5	12
SRP_00383	Bacteria_small_SRP links to Rfam database...	0.92	0.92	0.92	22	3216	6	0	2	4	2

^top

Performance of IPknot - scored lower in this pairwise comparison

1. Total counts & total scores for IPknot

Total Base Pair Counts
Total TP	3617
Total TN	854050
Total FP	1484
Total FP CONTRA	164
Total FP INCONS	965
Total FP COMP	355
Total FN	1493

Total Scores
MCC	0.733
Average MCC ± 95% Confidence Intervals	0.704 ± 0.039
Sensitivity	0.708
Positive Predictive Value	0.762
Nr of predictions	216

^top

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

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
ASE_00251	RNaseP_nuc links to Rfam database...	1.00	1.00	1.00	43	17723	18	0	0	18	0
PDB_00005	Tymo_tRNA-like links to Rfam database...	0.71	0.71	0.71	10	932	4	0	4	0	4
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...	0.94	0.88	1.00	36	5014	0	0	0	0	5
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	21	0	21	0	23
PDB_00741	Entero_5_CRE links to Rfam database...	0.87	0.76	1.00	13	690	0	0	0	0	4
PDB_00810	s2m links to Rfam database...	0.91	0.82	1.00	14	1067	0	0	0	0	3
PDB_00828	Purine links to Rfam database...	0.90	0.81	1.00	22	2463	0	0	0	0	5
PDB_00829	Purine links to Rfam database...	0.86	0.75	1.00	18	2260	0	0	0	0	6
PDB_00876	HIV_FE links to Rfam database...	0.97	0.95	1.00	19	971	0	0	0	0	1
PDB_01001	tRNA links to Rfam database...	0.91	0.83	1.00	15	2130	0	0	0	0	3
PDB_01020	Purine links to Rfam database...	0.86	0.74	1.00	17	2261	1	0	0	1	6
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...	0.96	0.92	1.00	12	891	4	0	0	4	1
PDB_01073	SAM links to Rfam database...	0.80	0.65	1.00	22	4349	1	0	0	1	12
PDB_01092	glmS links to Rfam database...	0.73	0.63	0.85	33	10114	8	1	5	2	19
PDB_01114	TPP links to Rfam database...	0.56	0.48	0.65	13	2830	7	0	7	0	14
PDB_01152	HIV_FS2 links to Rfam database...	0.88	0.79	1.00	11	550	0	0	0	0	3
PDB_01236	ykoK links to Rfam database...	0.73	0.67	0.80	36	11583	12	0	9	3	18
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...	0.80	0.80	0.80	12	1416	5	3	0	2	3
RFA_00396	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1417	1	0	0	1	1
RFA_00402	Hammerhead_3 links to Rfam database...	0.33	0.33	0.33	5	1416	11	0	10	1	10
RFA_00409	Hammerhead_3 links to Rfam database...	0.76	0.73	0.79	11	1417	4	1	2	1	4
RFA_00416	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1470	3	0	0	3	0
RFA_00425	Hammerhead_3 links to Rfam database...	0.64	0.60	0.69	9	1640	9	0	4	5	6
RFA_00427	Hammerhead_3 links to Rfam database...	0.97	0.93	1.00	14	1471	2	0	0	2	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_00444	Hammerhead_3 links to Rfam database...	1.00	1.00	1.00	15	1525	1	0	0	1	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...	0.77	0.60	1.00	9	1476	2	0	0	2	6
RFA_00582	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	5980	19	0	0	19	0
RFA_00583	Y_RNA links to Rfam database...	0.93	0.93	0.93	14	4935	9	0	1	8	1
RFA_00584	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	2911	12	0	0	12	0
RFA_00585	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	4	0	0	4	0
RFA_00586	Y_RNA links to Rfam database...	0.97	0.93	1.00	14	3902	10	0	0	10	1
RFA_00587	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4836	8	0	0	8	0
RFA_00588	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4545	11	0	0	11	0
RFA_00589	Y_RNA links to Rfam database...	1.00	1.00	1.00	15	4356	17	0	0	17	0
RFA_00594	Y_RNA links to Rfam database...	0.90	0.87	0.93	13	2761	4	0	1	3	2
RFA_00596	Y_RNA links to Rfam database...	0.00	0.00	0.00	0	5988	18	3	4	11	15
RFA_00603	Telomerase-cil links to Rfam database...	0.68	0.71	0.66	25	13492	15	4	9	2	10
RFA_00604	Telomerase-cil links to Rfam database...	0.75	0.74	0.76	26	13496	19	2	6	11	9
RFA_00605	Telomerase-cil links to Rfam database...	0.36	0.34	0.39	12	15194	27	2	17	8	23
RFA_00607	Telomerase-cil links to Rfam database...	0.91	0.83	1.00	30	17736	7	0	0	7	6
RFA_00609	Telomerase-cil links to Rfam database...	0.87	0.89	0.85	33	17916	14	2	4	8	4
RFA_00610	Telomerase-cil links to Rfam database...	0.90	0.86	0.94	32	17171	12	0	2	10	5
RFA_00611	Telomerase-cil links to Rfam database...	0.86	0.74	1.00	26	13015	0	0	0	0	9
RFA_00613	Telomerase-cil links to Rfam database...	0.61	0.49	0.77	17	12858	5	4	1	0	18
RFA_00615	Telomerase-cil links to Rfam database...	0.71	0.66	0.77	23	13336	7	3	4	0	12
RFA_00632	HDV_ribozyme links to Rfam database...	0.42	0.36	0.50	10	4075	11	0	10	1	18
RFA_00636	HDV_ribozyme links to Rfam database...	0.65	0.64	0.67	18	3978	9	3	6	0	10
RFA_00642	Vimentin3 links to Rfam database...	0.21	0.17	0.27	3	2915	8	0	8	0	15
RFA_00643	Vimentin3 links to Rfam database...	0.19	0.17	0.23	3	2198	10	0	10	0	15
RFA_00644	Vimentin3 links to Rfam database...	0.28	0.22	0.36	4	2690	7	4	3	0	14
RFA_00645	Vimentin3 links to Rfam database...	-0.01	0.00	0.00	0	2405	10	2	8	0	18
RFA_00649	Vimentin3 links to Rfam database...	0.53	0.28	1.00	5	2140	0	0	0	0	13
RFA_00651	Vimentin3 links to Rfam database...	0.31	0.22	0.44	4	2071	6	0	5	1	14
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...	-0.01	0.00	0.00	0	2400	15	2	13	0	18
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...	0.29	0.29	0.31	4	977	10	1	8	1	10
RFA_00668	Hammerhead_1 links to Rfam database...	0.65	0.43	1.00	6	984	0	0	0	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...	0.46	0.43	0.50	6	1116	7	0	6	1	8
RFA_00675	Hammerhead_1 links to Rfam database...	-0.01	0.00	0.00	0	980	11	0	10	1	14
RFA_00677	Hammerhead_1 links to Rfam database...	0.48	0.43	0.55	6	979	6	0	5	1	8
RFA_00678	Hammerhead_1 links to Rfam database...	0.53	0.29	1.00	4	942	0	0	0	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...	0.50	0.36	0.71	5	983	3	0	2	1	9
RFA_00695	Hammerhead_1 links to Rfam database...	0.36	0.29	0.44	4	7012	22	1	4	17	10
RFA_00703	Hammerhead_1 links to Rfam database...	0.44	0.43	0.46	6	4265	19	1	6	12	8
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...	0.74	0.71	0.77	10	1022	4	0	3	1	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	1030	5	0	5	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...	0.08	0.07	0.11	1	981	9	0	8	1	13
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...	0.80	0.64	1.00	9	894	0	0	0	0	5
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...	0.64	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...	1.00	1.00	1.00	12	891	1	0	0	1	0
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...	0.74	0.56	1.00	10	1881	0	0	0	0	8
RFA_00768	Corona_pk3 links to Rfam database...	1.00	1.00	1.00	18	1873	0	0	0	0	0
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...	0.64	0.50	0.82	9	2005	4	0	2	2	9
RFA_00773	Corona_pk3 links to Rfam database...	0.61	0.56	0.67	10	1938	8	1	4	3	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...	0.97	0.94	1.00	30	5020	0	0	0	0	2
RFA_00786	Gammaretro_CES links to Rfam database...	0.34	0.31	0.38	10	5024	16	1	15	0	22
RFA_00791	Gammaretro_CES links to Rfam database...	0.54	0.56	0.53	18	5117	16	6	10	0	14
RFA_00792	Gammaretro_CES links to Rfam database...	0.91	0.91	0.91	29	5018	3	2	1	0	3
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...	0.75	0.56	1.00	9	2007	0	0	0	0	7
RFA_00809	RydC links to Rfam database...	0.47	0.38	0.60	6	2135	4	0	4	0	10
SPR_00020	tRNA links to Rfam database...	0.80	0.80	0.80	16	2681	5	1	3	1	4
SPR_00023	tRNA links to Rfam database...	0.51	0.52	0.50	11	2828	11	2	9	0	10
SPR_00137	tRNA links to Rfam database...	0.77	0.86	0.69	18	2900	13	4	4	5	3
SPR_00273	tRNA links to Rfam database...	0.58	0.57	0.60	12	2830	8	1	7	0	9
SPR_00277	tRNA links to Rfam database...	1.00	1.00	1.00	21	2905	0	0	0	0	0
SPR_00394	tRNA links to Rfam database...	0.63	0.57	0.71	12	3638	5	4	1	0	9
SPR_00402	tRNA links to Rfam database...	0.79	0.62	1.00	13	2543	0	0	0	0	8
SPR_00721	tRNA links to Rfam database...	0.71	0.76	0.67	16	2902	8	2	6	0	5
SPR_00816	tRNA links to Rfam database...	0.36	0.35	0.37	7	3467	15	3	9	3	13
SPR_01157	tRNA links to Rfam database...	0.88	0.90	0.86	19	2753	4	0	3	1	2
SRP_00001	Bacteria_large_SRP links to Rfam database...	0.94	0.95	0.93	38	6745	3	1	2	0	2
SRP_00008	Bacteria_small_SRP links to Rfam database...	1.00	1.00	1.00	25	2901	0	0	0	0	0
SRP_00020	Bacteria_small_SRP links to Rfam database...	0.89	0.91	0.88	30	5531	4	1	3	0	3
SRP_00038	Bacteria_small_SRP links to Rfam database...	0.23	0.24	0.24	8	5016	26	2	24	0	25
SRP_00040	Bacteria_small_SRP links to Rfam database...	0.70	0.74	0.66	23	5530	14	1	11	2	8
SRP_00042	Bacteria_small_SRP links to Rfam database...	0.62	0.60	0.65	15	3982	9	0	8	1	10
SRP_00043	Bacteria_small_SRP links to Rfam database...	0.48	0.48	0.48	14	5021	18	3	12	3	15
SRP_00044	Bacteria_small_SRP links to Rfam database...	0.92	0.94	0.91	30	6072	6	1	2	3	2
SRP_00046	Bacteria_small_SRP links to Rfam database...	0.97	0.97	0.97	31	4721	2	0	1	1	1
SRP_00051	Bacteria_small_SRP links to Rfam database...	0.61	0.53	0.70	16	5437	9	2	5	2	14
SRP_00054	Bacteria_small_SRP links to Rfam database...	0.35	0.34	0.37	11	5535	19	0	19	0	21
SRP_00056	Bacteria_small_SRP links to Rfam database...	0.81	0.81	0.81	30	6404	7	1	6	0	7
SRP_00057	Bacteria_small_SRP links to Rfam database...	0.83	0.83	0.83	29	6293	7	1	5	1	6
SRP_00058	Bacteria_small_SRP links to Rfam database...	0.93	0.94	0.91	32	5743	7	1	2	4	2
SRP_00067	Bacteria_small_SRP links to Rfam database...	0.75	0.71	0.79	27	5744	7	1	6	0	11
SRP_00072	Bacteria_small_SRP links to Rfam database...	0.33	0.31	0.36	9	6303	17	1	15	1	20
SRP_00074	Bacteria_small_SRP links to Rfam database...	0.16	0.17	0.16	5	6524	30	4	22	4	24
SRP_00075	Bacteria_small_SRP links to Rfam database...	0.79	0.79	0.79	27	5531	10	0	7	3	7
SRP_00077	Bacteria_small_SRP links to Rfam database...	0.65	0.62	0.68	23	6636	12	2	9	1	14
SRP_00081	Bacteria_small_SRP links to Rfam database...	0.69	0.74	0.64	23	5529	13	1	12	0	8
SRP_00084	Bacteria_small_SRP links to Rfam database...	0.90	0.91	0.89	31	5425	4	1	3	0	3
SRP_00094	Bacteria_small_SRP links to Rfam database...	0.84	0.88	0.81	21	4069	5	1	4	0	3
SRP_00095	Bacteria_small_SRP links to Rfam database...	0.72	0.72	0.72	18	3980	7	2	5	0	7
SRP_00098	Bacteria_small_SRP links to Rfam database...	0.81	0.81	0.81	30	6404	8	0	7	1	7
SRP_00105	Bacteria_small_SRP links to Rfam database...	0.96	0.94	0.97	32	5532	1	0	1	0	2
SRP_00106	Bacteria_large_SRP links to Rfam database...	0.67	0.76	0.59	19	5221	16	5	8	3	6
SRP_00107	Bacteria_small_SRP links to Rfam database...	0.28	0.32	0.25	6	3631	20	4	14	2	13
SRP_00121	Bacteria_small_SRP links to Rfam database...	0.61	0.60	0.63	15	4254	9	0	9	0	10
SRP_00128	Bacteria_small_SRP links to Rfam database...	0.76	0.81	0.73	29	6746	11	1	10	0	7
SRP_00132	Bacteria_small_SRP links to Rfam database...	0.69	0.72	0.66	21	4819	14	0	11	3	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...	0.74	0.84	0.66	21	4154	11	4	7	0	4
SRP_00141	Bacteria_small_SRP links to Rfam database...	0.95	0.95	0.95	39	6287	2	1	1	0	2
SRP_00145	Bacteria_small_SRP links to Rfam database...	0.96	0.98	0.95	39	6287	2	1	1	0	1
SRP_00146	Bacteria_small_SRP links to Rfam database...	0.87	0.83	0.91	30	5220	3	1	2	0	6
SRP_00161	Bacteria_small_SRP links to Rfam database...	0.86	0.86	0.86	19	2828	3	0	3	0	3
SRP_00162	Bacteria_small_SRP links to Rfam database...	0.89	0.91	0.88	21	2902	4	0	3	1	2
SRP_00163	Bacteria_small_SRP links to Rfam database...	0.84	0.88	0.79	23	3457	6	2	4	0	3
SRP_00164	Bacteria_small_SRP links to Rfam database...	0.82	0.83	0.81	29	6867	7	1	6	0	6
SRP_00170	Bacteria_small_SRP links to Rfam database...	0.59	0.60	0.58	15	4069	12	0	11	1	10
SRP_00194	Bacteria_small_SRP links to Rfam database...	0.77	0.81	0.74	17	3217	6	0	6	0	4
SRP_00200	Bacteria_small_SRP links to Rfam database...	0.79	0.81	0.78	29	6866	8	1	7	0	7
SRP_00209	Bacteria_small_SRP links to Rfam database...	0.65	0.67	0.64	18	4628	11	1	9	1	9
SRP_00213	Bacteria_small_SRP links to Rfam database...	0.78	0.80	0.77	20	4160	6	1	5	0	5
SRP_00215	Bacteria_small_SRP links to Rfam database...	0.82	0.80	0.83	20	3216	4	0	4	0	5
SRP_00216	Bacteria_small_SRP links to Rfam database...	0.95	0.96	0.93	26	3375	3	1	1	1	1
SRP_00217	Bacteria_small_SRP links to Rfam database...	0.66	0.67	0.67	16	3297	9	0	8	1	8
SRP_00219	Bacteria_small_SRP links to Rfam database...	0.94	0.96	0.92	22	3297	3	0	2	1	1
SRP_00222	Bacteria_small_SRP links to Rfam database...	0.94	0.96	0.92	24	3055	3	1	1	1	1
SRP_00227	Bacteria_small_SRP links to Rfam database...	0.92	0.94	0.91	29	5119	3	1	2	0	2
SRP_00229	Bacteria_small_SRP links to Rfam database...	0.54	0.56	0.54	15	5225	15	0	13	2	12
SRP_00231	Bacteria_small_SRP links to Rfam database...	0.93	0.94	0.91	32	5425	3	1	2	0	2
SRP_00233	Bacteria_small_SRP links to Rfam database...	0.89	0.85	0.93	28	5121	2	0	2	0	5
SRP_00243	Bacteria_small_SRP links to Rfam database...	0.97	0.94	1.00	29	5122	1	0	0	1	2
SRP_00244	Bacteria_small_SRP links to Rfam database...	0.90	0.90	0.90	35	6864	4	2	2	0	4
SRP_00250	Bacteria_small_SRP links to Rfam database...	0.78	0.81	0.76	29	6748	11	1	8	2	7
SRP_00251	Bacteria_small_SRP links to Rfam database...	0.75	0.78	0.72	28	6982	11	1	10	0	8
SRP_00266	Bacteria_small_SRP links to Rfam database...	0.76	0.72	0.81	21	4630	6	0	5	1	8
SRP_00268	Bacteria_small_SRP links to Rfam database...	0.76	0.70	0.83	19	4163	4	1	3	0	8
SRP_00269	Bacteria_small_SRP links to Rfam database...	0.42	0.39	0.45	13	5021	16	2	14	0	20
SRP_00270	Bacteria_small_SRP links to Rfam database...	0.43	0.45	0.41	14	4622	20	2	18	0	17
SRP_00271	Bacteria_small_SRP links to Rfam database...	-0.01	0.00	0.00	0	3217	23	1	22	0	24
SRP_00273	Bacteria_small_SRP links to Rfam database...	0.91	0.93	0.90	37	6745	5	1	3	1	3
SRP_00274	Bacteria_small_SRP links to Rfam database...	0.93	0.95	0.92	36	6864	3	1	2	0	2
SRP_00285	Bacteria_small_SRP links to Rfam database...	0.95	0.93	0.97	28	3712	1	0	1	0	2
SRP_00295	Bacteria_small_SRP links to Rfam database...	0.96	0.97	0.95	37	6864	3	1	1	1	1
SRP_00303	Bacteria_small_SRP links to Rfam database...	0.81	0.84	0.77	27	6635	8	1	7	0	5
SRP_00310	Bacteria_small_SRP links to Rfam database...	0.87	0.87	0.87	20	2903	4	0	3	1	3
SRP_00312	Bacteria_small_SRP links to Rfam database...	0.38	0.37	0.40	10	4161	15	3	12	0	17
SRP_00315	Bacteria_small_SRP links to Rfam database...	0.87	0.87	0.87	20	2903	3	0	3	0	3
SRP_00318	Bacteria_small_SRP links to Rfam database...	0.87	0.87	0.87	20	2980	3	0	3	0	3
SRP_00324	Bacteria_small_SRP links to Rfam database...	0.62	0.62	0.62	18	5327	11	3	8	0	11
SRP_00325	Bacteria_small_SRP links to Rfam database...	0.95	0.94	0.97	31	4339	1	0	1	0	2
SRP_00326	Bacteria_small_SRP links to Rfam database...	0.80	0.84	0.76	26	5016	8	3	5	0	5
SRP_00333	Bacteria_small_SRP links to Rfam database...	0.89	0.85	0.94	29	5120	2	0	2	0	5
SRP_00338	Bacteria_small_SRP links to Rfam database...	0.97	0.97	0.97	35	5424	1	0	1	0	1
SRP_00341	Bacteria_small_SRP links to Rfam database...	0.53	0.55	0.52	17	4720	16	0	16	0	14
SRP_00342	Bacteria_small_SRP links to Rfam database...	0.59	0.60	0.58	15	3979	16	1	10	5	10
SRP_00350	Bacteria_small_SRP links to Rfam database...	0.48	0.41	0.58	11	3897	8	0	8	0	16
SRP_00356	Bacteria_small_SRP links to Rfam database...	0.80	0.80	0.80	24	5020	6	2	4	0	6
SRP_00357	Bacteria_small_SRP links to Rfam database...	0.96	0.97	0.95	35	5319	2	1	1	0	1
SRP_00358	Bacteria_small_SRP links to Rfam database...	0.96	0.97	0.94	34	6292	2	1	1	0	1
SRP_00363	Bacteria_small_SRP links to Rfam database...	0.95	0.97	0.94	29	4722	4	0	2	2	1
SRP_00365	Bacteria_small_SRP links to Rfam database...	0.94	0.93	0.96	25	3377	1	0	1	0	2
SRP_00367	Bacteria_small_SRP links to Rfam database...	0.83	0.86	0.81	30	6749	7	1	6	0	5
SRP_00369	Bacteria_small_SRP links to Rfam database...	0.93	0.94	0.92	33	5742	4	1	2	1	2
SRP_00383	Bacteria_small_SRP links to Rfam database...	0.04	0.04	0.05	1	3220	19	3	16	0	23

^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 CentroidAlifold(seed) - scored higher in this pairwise comparison

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

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

Performance of IPknot - scored lower in this pairwise comparison

1. Total counts & total scores for IPknot

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