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 3 Comparison of sampling quality for tRNAs

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	—	0.2413	0.4082	0.5548	0.5548	0.5552	0.6278
	mep (0.5)	0.2409	0.4068	0.5548	0.5548	0.5552	0.6265
	mep (0.99)	0.1877	0.3551	0.5382	0.5382	0.5386	0.6075
	fep (0.5)	0.2339	0.4017	0.5511	0.5511	0.5516	0.6269
	fep (0.99)	0.0014	0.0384	0.1979	0.1979	0.1984	0.2326
LSCFG	—	0.3324	0.4956	0.6574	0.6574	0.6579	0.7351
	mep (0.5)	0.3324	0.4956	0.6574	0.6574	0.6579	0.7351
	mep (0.99)	0.3236	0.4892	0.6560	0.6560	0.6565	0.7332
	fep (0.5)	0.3324	0.4966	0.6588	0.6588	0.6593	0.7369
	fep (0.99)	0.0624	0.2626	0.6246	0.6250	0.6250	0.6967
		(b) CSP _freq values (for selection principle MF struct.)
Approach	Errors			Shape level
		0	1	2	3	4	5
SCFG	—	0.2099	0.3699	0.5594	0.5594	0.5599	0.6302
	mep (0.5)	0.1683	0.3301	0.5372	0.5372	0.5377	0.6047
	mep (0.99)	0.0522	0.1822	0.4517	0.4517	0.4517	0.5215
	fep (0.5)	0.1049	0.2547	0.5155	0.5155	0.5160	0.5793
	fep (0.99)	0.0000	0.0125	0.1110	0.1110	0.1119	0.2062
LSCFG	—	0.3269	0.4892	0.6560	0.6565	0.6565	0.7337
	mep (0.5)	0.2534	0.4235	0.6708	0.6708	0.6713	0.7485
	mep (0.99)	0.1137	0.2954	0.6801	0.6801	0.6801	0.7568
	fep (0.5)	0.1794	0.3653	0.6704	0.6704	0.6709	0.7531
	fep (0.99)	0.0023	0.1262	0.6334	0.6334	0.6357	0.7240
		(c) CSP _freq values (for selection principle MEA struct.)
Approach	Errors			Shape level
		0	1	2	3	4	5
SCFG	—	0.0555	0.2094	0.4193	0.4193	0.4207	0.4679
	mep (0.5)	0.0416	0.1817	0.4045	0.4045	0.4055	0.4489
	mep (0.99)	0.0125	0.0989	0.3112	0.3112	0.3126	0.3570
	fep (0.5)	0.0245	0.1364	0.3662	0.3662	0.3666	0.4059
	fep (0.99)	0.0000	0.0014	0.0245	0.0245	0.0250	0.0546
LSCFG	—	0.1854	0.3574	0.4919	0.4919	0.4919	0.5465
	mep (0.5)	0.1405	0.3056	0.4998	0.4998	0.4998	0.5567
	mep (0.99)	0.0730	0.2191	0.4753	0.4753	0.4753	0.5284
	fep (0.5)	0.1003	0.2556	0.4836	0.4836	0.4836	0.5409
	fep (0.99)	0.0009	0.0781	0.3902	0.3902	0.3921	0.4508
		(d) CSP _freq values (for selection principle Centroid)
Approach	Errors			Shape level
		0	1	2	3	4	5
SCFG	—	0.0374	0.1276	0.2973	0.2973	0.2977	0.3130
	mep (0.5)	0.0273	0.1045	0.2779	0.2779	0.2783	0.2908
	mep (0.99)	0.0083	0.0541	0.2007	0.2007	0.2007	0.2173
	fep (0.5)	0.0134	0.0795	0.2473	0.2473	0.2473	0.2603
	fep (0.99)	0.0000	0.0009	0.0120	0.0120	0.0120	0.0227
LSCFG	—	0.1729	0.3158	0.4300	0.4300	0.4300	0.4762
	mep (0.5)	0.1322	0.2728	0.4374	0.4374	0.4374	0.4859
	mep (0.99)	0.0693	0.1914	0.4101	0.4101	0.4101	0.4558
	fep (0.5)	0.0957	0.2261	0.4207	0.4207	0.4207	0.4642
	fep (0.99)	0.0009	0.0633	0.3264	0.3264	0.3269	0.3648

Tables record specific values related to shapes of predictions and sampled structures, obtained from our tRNA 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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