Comprehensive comparison of graph based multiple protein sequence alignment strategies

BMC Bioinformatics

Table 5 Iterative refinement versus consistency, compared on BAliBASE

Strategy	RV11 (38)		RV12 (44)		RV20 (41)		RV30 (30)		RV40 (49)		RV50 (16)		Overall (218)		Time (sec)
	SP	%basic	SP	%basic	SP	%basic	SP	%basic	SP	%basic	SP	%basic	SP	%basic
basic	0.587	100.0	0.908	100.0	0.902	100.0	0.832	100.0	0.884	100.0	0.871	100.0	0.831	100.0	24.4
random × 100	0.623	106.1	0.922	101.5	0.902	100.0	0.832	100.0	0.885	100.1	0.871	100.0	0.839	101.0	40.6
tree_Random× 100	0.625	106.4	0.929	102.3	0.918	101.7	0.846	101.6	0.909	102.8	0.890	102.2	0.853	102.6	39.4
tree_BFS× 100	0.626	106.5	0.927	102.1	0.916	101.5	0.846	101.6	0.912	103.2	0.898	103.1	0.854	102.8	54.1
triplet_SeqAn	0.642	109.3	0.929	102.3	0.918	101.8	0.839	100.8	0.911	103.1	0.895	102.7	0.856	103.0	44.8
triplet_SeqAn+ tree_BFS× 100	0.643	109.5	0.930	102.4	0.917	101.7	0.842	101.1	0.909	102.8	0.894	102.6	0.856	103.0	195.4

Columns show the average sum-of-pairs (SP) score and the percentage value of the SP score relative to the basic strategy (%basic) achieved by each alignment strategy 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

ISSN: 1471-2105