Vertical decomposition with Genetic Algorithm for Multiple Sequence Alignment

BMC Bioinformatics

Table 6 Experiments on Selected Datasets of MSA-GA

Reference No.	Name of Dataset	MSA-GA	MSA-GA w/prealign	ClUSTAL W	VDGA_ Decomp_2	VDGA_Decomp_3	VDGA_Decomp_4
Ref. 1	1idy	0.427	0.438	0.500	0.550	0.651	0.654
	1tvxA	0.295	0.209	0.042	0.316	0.316	0.310
	1uky	0.443	0.405	0.392	0.416	0.459	0.464
	Kinase	0.295	0.488	0.479	0.531	0.545	0.548
	1ped	0.501	0.687	0.592	0.443	0.482	0.451
	2myr	0.212	0.302	0.296	0.347	0.359	0.282
	1ycc	0.650	0.653	0.643	0.752	0.839	0.685
	3cyr	0.772	0.789	0.767	0.797	0.898	0.797
	1ad2	0.821	0.845	0.773	0.959	0.950	0.941
	1ldg	0.895	0.922	0.880	0.914	0.946	0.903
	1fieA	0.843	0.942	0.932	0.926	0.960	0.927
	1sesA	0.620	0.913	0.913	0.917	0.962	0.923
	1krn	0.908	0.895	0.895	0.942	0.960	0.892
	2fxb	0.941	0.985	0.985	0.978	0.978	0.978
	1amk	0.965	0.959	0.945	0.982	0.984	0.982
	1ar5A	0.812	0.946	0.946	0.942	0.968	0.954
	1gpb	0.868	0.948	0.947	0.976	0.984	0.983
	1taq	0.525	0.826	0.826	0.938	0.959	0.944
Ref. 2	2pia	0.761	0.768	0.766	0.847	0.850	0.839
	1pamA	0.755	0.758	0.757	0.857	0.863	0.853
Ref. 3	Kinase	0.58	0.619	0.619	0.870	0.890	0.887
	1pamA	0.703	0.744	0.743	0.853	0.788	0.792
Ref. 4	1dynA	0.038	0.034	0.000	0.029	0.033	0.031
	Kinase2	0.71	0.635	0.630	0.330	0.542	0.478
Ref. 5	2cba	0.422	0.621	0.628	0.839	0.835	0.846
	S51	0.528	0.73	0.75	0.650	0.743	0.756
Average Score		0.627	0.695	0.679	0.727	0.744	0.735

ISSN: 1471-2105