Vertical decomposition with Genetic Algorithm for Multiple Sequence Alignment

Naznin, Farhana; Sarker, Ruhul; Essam, Daryl

doi:10.1186/1471-2105-12-353

BMC Bioinformatics

Table 7 Experiments on Reference 2 Datasets of BAliBase

From: Vertical decomposition with Genetic Algorithm for Multiple Sequence Alignment

Reference No.	Name of Dataset	PRRP	CLUSTALX	SAGA	DIALIGN	HMMT	SB_PIMA	ML_PIMA	MULTALIGN	PILEUP8	RBT-GA	VDGA_Decomp_2	VDGA_Decomp_3	VDGA_Decomp_4
Ref. 2	1aboA	0.256	0.65	0.489	0.384	0.724	0.391	0.22	0.528	0.000	0.812	0.723	0.791	0.679
	1idy	0.37	0.515	0.548	0.000	0.353	0.000	0.000	0.401	0.000	0.997	0.981	0.992	0.992
	1csy	0.35	0.154	0.154	0.000	0.000	0.000	0.000	0.154	0.114	0.735	0.731	0.885	0.831
	1r69	0.675	0.675	0.475	0.675	0.000	0.675	0.675	0.675	0.45	0.9	0.859	0.934	0.874
	1tvxA	0.207	0.552	0.448	0.000	0.276	0.241	0.241	0.138	0.345	0.891	0.944	0.974	0.944
	1tgxA	0.695	0.727	0.773	0.63	0.622	0.678	0.543	0.696	0.318	0.835	0.867	0.878	0.850
	1ubi	0.056	0.482	0.492	0.000	0.053	0.129	0.129	0.000	0.000	0.795	0.732	0.778	0.794
	1wit	0.76	0.557	0.694	0.724	0.641	0.469	0.463	0.5	0.476	0.825	0.875	0.815	0.774
	2trx	0.87	0.87	0.87	0.734	0.739	0.85	0.702	0.87	0.87	0.982	0.959	0.986	0.986
	1sbp	0.231	0.217	0.374	0.043	0.214	0.043	0.054	0.186	0.177	0.778	0.782	0.772	0.778
	1havA	0.52	0.48	0.448	0.000	0.194	0.259	0.238	0.5	0.493	0.792	0.884	0.846	0.884
	1uky	0.351	0.656	0.476	0.216	0.395	0.256	0.306	0.585	0.562	0.625	0.845	0.891	0.872
	2hsdA	0.404	0.484	0.498	0.262	0.423	0.39	0.561	0.593	0.278	0.745	0.856	0.829	0.742
	2pia	0.767	0.752	0.763	0.612	0.647	0.73	0.695	0.765	0.766	0.730	0.847	0.850	0.839
	3grs	0.363	0.192	0.282	0.350	0.141	0.183	0.211	0.192	0.159	0.755	0.717	0.751	0.781
	Kinase	0.896	0.848	0.867	0.692	0.749	0.755	0.651	0.83	0.799	0.712	0.825	0.888	0.812
	1ajsA	0.227	0.324	0.311	0.000	0.242	0.000	0.000	0.311	0.227	0.892	0.906	0.905	0.902
	1cpt	0.821	0.66	0.776	0.425	0.388	0.184	0.277	0.777	0.688	0.584	0.869	0.812	0.853
	1lvl	0.772	0.746	0.726	0.783	0.539	0.62	0.688	0.614	0.678	0.567	0.803	0.819	0.816
	1pamA	0.711	0.761	0.623	0.576	0.53	0.393	0.386	0.566	0.702	0.66	0.857	0.863	0.853
	1ped	0.881	0.834	0.835	0.773	0.696	0.651	0.647	0.741	0.749	0.78	0.935	0.947	0.943
	2myr	0.582	0.904	0.825	0.84	0.443	0.727	0.75	0.894	0.786	0.675	0.806	0.830	0.808
	4enl	0.668	0.375	0.739	0.122	0.213	0.096	0.092	0.384	0.224	0.812	0.890	0.889	0.899
Average Score		0.541	0.583	0.586	0.384	0.401	0.379	0.371	0.517	0.429	0.777	0.848	0.866	0.849

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ISSN: 1471-2105

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