Optimizing substitution matrix choice and gap parameters for sequence alignment

BMC Bioinformatics

Table 1 Training set accuracy

Set	Model	POP	IPA	>Acc
Bali	g2	80.3%	80.0%	0.4%
Bali	g4	80.6%	79.6%	1.3%
TermGaps	g2	80.2%	79.7%	0.6%
TermGaps	g4	84.0%	83.8%	0.2%

Training set accuracy (Q) for the g2 and g4 models on Bali and TermGaps using BLOSUM62 1/3-bit units. in The numbers in the POP and IPA columns are the Q values achieved by the gap para-meters reported by each method. In all cases, POP achieves higher accuracy, the >Acc column shows the amount by which the POP accuracy is better than IPA.

ISSN: 1471-2105