Table 2.

Substitution scoring matrices set used in homology search performance evaluation.

Matrix Sets	Algorithm	Matrix Numbers
EDSSMat Matrices	EDSSMat	50, 60, 62,70, 75, 80, 90
Standard Matrices	BLOSUM	30, 50, 62, 80
	PAM	120, 250
	MD	10, 20, 40
	VTML	10, 20, 40, 80, 120, 160, 200
Disorder Matrices	DUNMat	—
	Disorder	40, 60, 85
	MidicMat	—