Comprehensive comparison of graph based multiple protein sequence alignment strategies

BMC Bioinformatics

Table 1 Comparing guiding tree performance on BAliBASE

	RV11 (38)		RV12 (44)		RV20 (41)		RV30 (30)		RV40 (49)		RV50 (16)		Overall (218)
Guiding tree	SP	TC	SP	TC	SP	TC	SP	TC	SP	TC	SP	TC	SP	TC	Time(sec)
NJ	0.554	0.275	0.877	0.664	0.881	0.280	0.798	0.366	0.864	0.413	0.855	0.450	0.805	0.408	23.71
MIN	0.587	0.286	0.908	0.772	0.902	0.357	0.832	0.457	0.884	0.483	0.871	0.540	0.831	0.483	24.00
MAX	0.575	0.284	0.901	0.744	0.888	0.313	0.822	0.393	0.850	0.385	0.839	0.389	0.813	0.418	23.30
UPGMA	0.585	0.302	0.905	0.761	0.891	0.329	0.828	0.431	0.863	0.422	0.859	0.469	0.822	0.452	23.32
WUPGMA	0.583	0.294	0.905	0.761	0.896	0.329	0.829	0.432	0.860	0.423	0.850	0.453	0.821	0.448	23.52

Columns show the average sum-of-pairs (SP) and true-column (TC) scores achieved by different alignment strategies for each of the six BAliBASE references. The number of alignments in each reference is given in parentheses. Overall values for the entire database are reported in addition to the mean execution time of each strategy. The best results in each column are shown in bold. The strategies differ in the algorithm used to build the guiding tree: neighbor joining (NJ), single linkage (MIN), complete linkage (MAX), UPGMA and weighted UPGMA (WUPGMA)

ISSN: 1471-2105