3.2.22 Parameter -M

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3.2.22 Parameter -M

Parameter -M

Function Specifies which protein scoring matrix to use

Default BLOSUM62

Input format String

Example To score alignment with PAM30 matrix, use: -M PAM30

Parameter	-M
Function	Specifies which protein scoring matrix to use
Default	BLOSUM62
Input format	String
Example	To score alignment with PAM30 matrix, use: -M PAM30

Note:

For protein alignment, BLAST only supports the following five matrices: BLOSUM45, BLOSUM62, BLOSUM80, PAM30, and PAM70. BLOSUM matrices were derived from actual un-gapped block alignments of sequences with indicated percentage of similarities ([3]). PAM matrices are derived from closely related sequences with greater than 90% of similarities ([2]). Less stringent PAM matrices were derived from PAM1 using mathematical extrapolation.

Tao Tao 2006-12-29