Return Point Accepted Mutation (PAM) scoring matrix
ScoringMatrix =
pam(N)
[ScoringMatrix, MatrixInfo]
= pam(N)
... = pam(N, ...'Extended', ExtendedValue,
...)
... = pam(N, ...'Order', OrderValue,
...)
N | Integer specifying the PAM scoring matrix to return.
Choices are Tip Entering a larger value for |
ExtendedValue | Controls the return of the ambiguous characters ( |
OrderValue | Character vector or string that controls the order of amino acids in the scoring
matrix. Choices are a character vector or string with at least the |
ScoringMatrix =
pam(N)N scoring matrix for amino acid sequences.
[ returns a
structure with information about the PAM matrix. The fields in the
structure are ScoringMatrix, MatrixInfo]
= pam(N)Name, Scale, Entropy, Expected,
and Order.
... = pam( calls N, ...'PropertyName', PropertyValue,
...)pam with optional properties
that use property name/property value pairs. You can specify one or
more properties in any order. Each PropertyName must
be enclosed in single quotation marks and is case insensitive. These
property name/property value pairs are as follows:
... = pam( controls the return of the ambiguous characters (N, ...'Extended', ExtendedValue,
...)B, Z,
and X), and the stop character (*),
in addition to the 20 standard amino acid characters.
Choices are true or false (default).
... = pam(
controls the order of amino acids in the returned scoring matrix. Choices are a character vector
or string with at least the N, ...'Order', OrderValue,
...)20 standard amino acids. The default ordering of
the output is A R N D C Q E G H I L K M F P S T W Y V B Z X *. If
OrderValue does not contain the extended characters
B, Z, X, and *, then
these characters are not returned.
PAM50 substitution matrix in 1/2 bit units,
Expected score = -3.70, Entropy = 2.00 bits,
Lowest score = -13, Highest score = 13.
PAM250 substitution matrix in 1/3 bit units,
Expected score = -0.844, Entropy = 0.354 bits,
Lowest score = -8, Highest score = 17.
Return the PAM50 matrix.
PAM50 = pam(50)
Return the PAM250 matrix and specify the order of amino acids in the matrix.
PAM250 = pam(250,'Order','CSTPAGNDEQHRKMILVFYW')