State of the art: refinement of multiple sequence alignments

BMC Bioinformatics

Table 1 Impact on alignment quality following refinement.

BAliBASE reference alignments	ClustalW				Dialign				Mafft
	Default	RASCAL	RF	REFINER	Default	RASCAL	RF	REFINER	Default	RASCAL	RF	REFINER
Reference 1	0.65	0.63	0.66	0.66	0.62	0.65	0.67	0.62	0.70	0.69	0.69	0.71
Reference 2	0.78	0.80	0.80	0.80	0.78	0.80	0.79	0.79	0.83	0.82	0.83	0.82
Reference 3	0.66	0.69	0.67	0.68	0.65	0.64	0.65	0.66	0.76	0.73	0.75	0.77
Reference 4	0.67	0.68	0.66	0.70	0.67	0.71	0.66	0.69	0.75	0.73	0.70	0.77
Reference 5	0.65	0.67	0.66	0.68	0.67	0.65	0.64	0.67	0.76	0.73	0.72	0.76
Average	0.682	0.694	0.69	0.704	0.678	0.690	0.682	0.692	0.760	0.740	0.738	0.766
Increment (%)	0	1.760	1.173	3.226	0.000	1.770	0.590	2.065	0.000	-2.632	-2.895	0.789
BAliBASE reference alignments	Muscle				Probcons				T-Coffee
	Default	RASCAL	RF	REFINER	Default	RASCAL	RF	REFINER	Default	RASCAL	RF	REFINER
Reference 1	0.66	0.66	0.67	0.67	0.72	0.72	0.70	0.73	0.68	0.68	0.69	0.68
Reference 2	0.80	0.81	0.80	0.80	0.83	0.83	0.82	0.82	0.81	0.83	0.82	0.82
Reference 3	0.71	0.71	0.71	0.73	0.76	0.73	0.75	0.77	0.63	0.62	0.62	0.64
Reference 4	0.71	0.72	0.68	0.72	0.77	0.75	0.71	0.77	0.71	0.71	0.70	0.72
Reference 5	0.70	0.71	0.67	0.71	0.76	0.74	0.71	0.75	0.73	0.73	0.69	0.74
Average	0.716	0.722	0.706	0.734	0.768	0.754	0.738	0.77	0.704	0.714	0.704	0.720
Increment (%)	0.000	0.838	-1.397	2.514	0.000	-1.823	-3.906	0.260	0.000	1.420	0.000	2.273

ISSN: 1471-2105