MTRAP: Pairwise sequence alignment algorithm by a new measure based on transition probability between two consecutive pairs of residues

Table 5 Average Q scores on the BAliBASE 3.0 database.

Method	Reference 1		Reference 2	Reference 3	Reference 5
	Equidistant Sequences		Family with	Divergent	Large
	V1:0-20%ID	V2:20-40%ID	"Orphans"	subfamilies	Insertions
TCoffee-MTRAP	0.752	0.943	0.947	0.873	0.892
TCoffee-Lu/Sze	0.695	0.937	0.939	0.851	0.879
TCoffee	0.692	0.936	0.940	0.849	0.874
MAFFT	0.722	0.901	0.945	0.864	0.900
DIALIGN*	0.566	0.860	0.883	0.766	0.861
MUSCLE	0.743	0.931	0.941	0.870	0.872
ClustalW2	0.654	0.903	0.922	0.821	0.805
Probcons	0.811	0.951	0.957	0.905	0.909
Probalign	0.728	0.947	0.945	0.876	0.893

The average Q scores of five reference BBS sets (described as being trimmed to homologous regions) on BAliBASE 3.0 are shown. For each reference, the better scores of the TCoffee modified by Lu/Sze algorithm (TCoffee-Lu/Sze) and the TCoffee modified by MTRAP algorithm (TCoffee-MTRAP) are in bold. The best scores of the other methods are also in bold. ID means a sequence identity of the reference alignment.
*DIALIGN reported critical errors for some testing data. Therefore, the scores of DIALIGN were calculated by the partial testing data.

ISSN: 1471-2105