Evaluating the effect of disturbed ensemble distributions on SCFG based statistical sampling of RNA secondary structures

Scheid, Anika; Nebel, Markus E

doi:10.1186/1471-2105-13-159

Table 4 Comparison of sampling quality for 5S rRNAs

From: Evaluating the effect of disturbed ensemble distributions on SCFG based statistical sampling of RNA secondary structures

	(a) CSP_freqvalues (for selection principle MP struct.)
Approach	Errors	Shape level
		0	1	2	3	4	5
SCFG	—	0.0000	0.0026	0.0052	0.0131	0.0366	0.7110
	mep (0.5)	0.0000	0.0009	0.0026	0.0113	0.0287	0.7128
	mep (0.99)	0.0000	0.0026	0.0044	0.0095	0.0227	0.6919
	fep (0.5)	0.0000	0.0017	0.0043	0.0113	0.0374	0.6954
	fep (0.99)	0.0000	0.0000	0.0000	0.0017	0.0096	0.5474
LSCFG	—	0.2141	0.4256	0.4744	0.4900	0.9408	0.9843
	mep (0.5)	0.2141	0.4256	0.4744	0.4900	0.9408	0.9843
	mep (0.99)	0.1941	0.4221	0.4761	0.4892	0.9452	0.9852
	fep (0.5)	0.2124	0.4248	0.4726	0.4883	0.9417	0.9852
	fep (0.99)	0.0209	0.3029	0.3725	0.4186	0.8529	0.9809
	(b) CSP _freq values (for selection principle MF struct.)
Approach	Errors	Shape level
		0	1	2	3	4	5
SCFG	—	0.0000	0.0026	0.0052	0.0131	0.0357	0.7128
	mep (0.5)	0.0000	0.0009	0.0026	0.0122	0.0305	0.7180
	mep (0.99)	0.0000	0.0026	0.0044	0.0105	0.0235	0.6902
	fep (0.5)	0.0000	0.0017	0.0043	0.0113	0.0383	0.6971
	fep (0.99)	0.0000	0.0000	0.0000	0.0035	0.0200	0.5439
LSCFG	—	0.2002	0.4256	0.4700	0.4866	0.9417	0.9861
	mep (0.5)	0.1332	0.3960	0.4439	0.4587	0.9434	0.9869
	mep (0.99)	0.0365	0.3630	0.4308	0.4491	0.9304	0.9861
	fep (0.5)	0.0801	0.3847	0.4404	0.4561	0.9400	0.9861
	fep (0.99)	0.0035	0.1497	0.2106	0.3325	0.5440	0.9730
	(c) CSP _freq values (for selection principle MEA struct.)
Approach	Errors	Shape level
		0	1	2	3	4	5
SCFG	—	0.0000	0.0000	0.0000	0.0000	0.0261	0.3821
	mep (0.5)	0.0000	0.0000	0.0000	0.0000	0.0209	0.3698
	mep (0.99)	0.0000	0.0000	0.0000	0.0000	0.0122	0.3003
	fep (0.5)	0.0000	0.0000	0.0000	0.0000	0.0252	0.3438
	fep (0.99)	0.0000	0.0000	0.0000	0.0000	0.0026	0.0444
LSCFG	—	0.1062	0.3891	0.4291	0.4378	0.9051	0.9835
	mep (0.5)	0.1010	0.3751	0.4134	0.4239	0.8921	0.9782
	mep (0.99)	0.0392	0.3429	0.3986	0.4213	0.8712	0.9791
	fep (0.5)	0.0740	0.3839	0.4239	0.4387	0.8877	0.9791
	fep (0.99)	0.0017	0.1358	0.1863	0.2942	0.4970	0.9634
	(d) CSP _freq values (for selection principle Centroid)
Approach	Errors	Shape level
		0	1	2	3	4	5
SCFG	—	0.0000	0.0000	0.0000	0.0000	0.0104	0.1097
	mep (0.5)	0.0000	0.0000	0.0000	0.0000	0.0104	0.1062
	mep (0.99)	0.0000	0.0000	0.0000	0.0000	0.0078	0.0827
	fep (0.5)	0.0000	0.0000	0.0000	0.0000	0.0061	0.0932
	fep (0.99)	0.0000	0.0000	0.0000	0.0000	0.0009	0.0078
LSCFG	—	0.0966	0.2916	0.3238	0.3316	0.8703	0.9686
	mep (0.5)	0.0879	0.3142	0.3516	0.3621	0.8625	0.9686
	mep (0.99)	0.0322	0.2924	0.3377	0.3595	0.8294	0.9651
	fep (0.5)	0.0662	0.3194	0.3551	0.3638	0.8512	0.9695
	fep (0.99)	0.0017	0.1053	0.1471	0.2219	0.4831	0.9339

Tables record specific values related to shapes of predictions and sampled structures, obtained from our 5S rRNA database. All results were computed by 10-fold cross-validation procedures, using sample size 1000 and min_hel= min_HL= 1.

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