Comprehensive comparison of graph based multiple protein sequence alignment strategies

BMC Bioinformatics

Table 3 Comparing score transformation strategies on BAliBASE

	RV11 (38)		RV12 (44)		RV20 (41)		RV30 (30)		RV40 (49)		RV50 (16)		Overall (218)
Strategy	SP	%basic	SP	%basic	SP	%basic	SP	%basic	SP	%basic	SP	%basic	SP	%basic	Time (sec)
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	24.44
maxflow	0.585	99.6	0.910	100.2	0.909	100.8	0.836	100.4	0.895	101.2	0.880	100.9	0.836	100.6	25.04
triplet_T-Coffee	0.613	104.4	0.914	100.6	0.914	101.3	0.840	100.9	0.901	101.9	0.888	101.9	0.845	101.7	27.85
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	44.83
triplet_SeqAn× 2	0.648	110.3	0.928	102.2	0.917	101.7	0.842	101.1	0.910	103.0	0.896	102.8	0.857	103.1	608.79
clique	0.530	90.2	0.896	98.7	0.820	90.9	0.614	73.7	0.758	85.8	0.675	77.4	0.715	86.1	1764.83
triplet_T-Coffee+ clique	0.637	108.4	0.930	102.4	0.919	101.8	0.839	100.8	0.905	102.4	0.885	101.6	0.852	102.6	1753.63
maxflow + clique	0.590	100.4	0.924	101.8	0.904	100.2	0.819	98.3	0.876	99.1	0.879	100.8	0.832	100.1	2337.67

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